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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
36 stars 20 forks source link

Please make sure that the read pairs have been mapped both, combined and on a per mate basis #101

Closed BirongZhang closed 2 years ago

BirongZhang commented 2 years ago

Hi DCC team,

Thanks for developing such as useful tool!

When I used it, I got some error: Here is my scripts:

# http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=1221177343_h3fzKaDey7mY9G3uYurJpQBBXJ1S&clade=mammal&org=Human&db=hg38&hgta_group=rep&hgta_track=knownGene&hgta_table=0&hgta_regionType=genome&position=chrX%3A15%2C560%2C138-15%2C602%2C945&hgta_outputType=primaryTable&hgta_outFileName=UCSC
sed -i  '' 's/^chr//g' GRCh38_repeat_file.gtf
head -3 GRCh38_repeat_file.gtf

# Preparation of input files for circRNA detection step
# step one: obtain reference genome: Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/

# step two: repeat masker file for the genome build: GRCh38_repeatmasker.gtf.gz
http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=1221177343_h3fzKaDey7mY9G3uYurJpQBBXJ1S&clade=mammal&org=Human&db=hg38&hgta_group=rep&hgta_track=knownGene&hgta_table=0&hgta_regionType=genome&position=chrX%3A15%2C560%2C138-15%2C602%2C945&hgta_outputType=primaryTable&hgta_outFileName=UCSC
https://www.biostars.org/p/227979/

DCC samplesheet \
      -mt1 meta1 \
      -mt2 meta2 \
      -D \
      -R GRCh38_repeat_file.gtf \
      -an GRCh38_repeatmasker.gtf \
      -Pi \
      -F \
      -M \
      -Nr 5 6 \
      -fg \
      -G \
      -O DCC \
      -A /scratch/c.c2050857/reference/reference_Human/Homo_sapiens.GRCh38.dna.primary_assembly.fa

Here is my STAR output:

head -3 samplesheet
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036347/SRR9036347_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036347/SRR9036347_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036334/SRR9036334_2_Chimeric.out.junction
(circtools-detect) [c.c2050857@cl2 Results]$ find -L /scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1 -name "*_1_Chimeric.out.junction" > meta1
(circtools-detect) [c.c2050857@cl2 Results]$ find -L /scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_2 -name "*_2_Chimeric.out.junction" > meta2
(circtools-detect) [c.c2050857@cl2 Results]$ head -3 meta1
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036347/SRR9036347_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036334/SRR9036334_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036315/SRR9036315_1_Chimeric.out.junction
(circtools-detect) [c.c2050857@cl2 Results]$ head -3 meta2
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_2/SRR9036347/SRR9036347_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_2/SRR9036334/SRR9036334_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_2/SRR9036315/SRR9036315_2_Chimeric.out.junction
Screenshot 2021-12-01 at 00 55 35

Here is my error:

DCC 0.5.0 started
44 CPU cores available, using 2
Please make sure that the read pairs have been mapped both, combined and on a per mate basis
Collecting chimera information from mates-separate mapping
WARNING: File meta2, line 1 does not contain all features.
WARNING: meta2 is probably corrupt.
WARNING: Offending line: /scratch/c.c2050857/NAFLD/GSE130970/Results/R2/SRR9036381_2_Chimeric.out.junction
Traceback (most recent call last):
  File "/nfshome/store03/users/c.c2050857/.venv-circtools-detect/bin/DCC", line 11, in <module>
    load_entry_point('DCC==0.5.0', 'console_scripts', 'DCC')()
  File "build/bdist.linux-x86_64/egg/DCC/main.py", line 254, in main
  File "build/bdist.linux-x86_64/egg/DCC/main.py", line 535, in fixall
  File "build/bdist.linux-x86_64/egg/DCC/fix2chimera.py", line 94, in fixchimerics
  File "build/bdist.linux-x86_64/egg/DCC/fix2chimera.py", line 65, in fixmate2
IndexError: list index out of range

Could you help me to take a look at this? Any advice would babe highly appreciated, thanks!

tjakobi commented 2 years ago

Hi @BirongZhang,

The main issue is probably this line:

Input file lists have different length (mate 1 78, mate 2 78, joined 156).

There should be only 78 lines in samplesheet, not 156.

Could you please paste the content of the samplesheet, meta1, and meta2?

Thank you,

Tobias

tjakobi commented 2 years ago

Seems like you updated the issue before I submitted my above response.

Given the new error message, please continue to use @samplesheet in the command line instead of samplesheet.

Moreover, the meta* files should only contain file names, not the complete path, DCC tries to get the path correct by itself.

Moreover, from the original post, I am not sure if your

BirongZhang commented 2 years ago

Hi Tobias，

Thanks so much for you efficient reply!

Sorry, I am newbie for Linux and DCC. I am still confused how to prepare those files.

Here is my samplesheet files (156 lines):

(circtools-detect) [c.c2050857@cl2 Results]$ cat samplesheet
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036347/SRR9036347_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036347/SRR9036347_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036334/SRR9036334_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036334/SRR9036334_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036315/SRR9036315_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036315/SRR9036315_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036367/SRR9036367_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036367/SRR9036367_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036365/SRR9036365_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036365/SRR9036365_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036371/SRR9036371_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036371/SRR9036371_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036350/SRR9036350_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036350/SRR9036350_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036336/SRR9036336_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036336/SRR9036336_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036326/SRR9036326_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036326/SRR9036326_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036337/SRR9036337_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036337/SRR9036337_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036354/SRR9036354_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036354/SRR9036354_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036368/SRR9036368_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036368/SRR9036368_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036344/SRR9036344_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036344/SRR9036344_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036364/SRR9036364_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036364/SRR9036364_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036342/SRR9036342_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036342/SRR9036342_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036329/SRR9036329_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036329/SRR9036329_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036363/SRR9036363_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036363/SRR9036363_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036307/SRR9036307_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036307/SRR9036307_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036356/SRR9036356_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036356/SRR9036356_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036312/SRR9036312_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036312/SRR9036312_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036353/SRR9036353_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036353/SRR9036353_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036382/SRR9036382_2_Chimeric.out.junction
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/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036321/SRR9036321_2_Chimeric.out.junction
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/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036374/SRR9036374_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036374/SRR9036374_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036348/SRR9036348_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036348/SRR9036348_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036346/SRR9036346_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036346/SRR9036346_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036309/SRR9036309_2_Chimeric.out.junction
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/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036308/SRR9036308_2_Chimeric.out.junction
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/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036352/SRR9036352_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036352/SRR9036352_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036318/SRR9036318_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036318/SRR9036318_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036340/SRR9036340_2_Chimeric.out.junction
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/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036376/SRR9036376_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036376/SRR9036376_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036343/SRR9036343_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036343/SRR9036343_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036366/SRR9036366_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036366/SRR9036366_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036384/SRR9036384_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036384/SRR9036384_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036359/SRR9036359_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036359/SRR9036359_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036333/SRR9036333_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036333/SRR9036333_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036325/SRR9036325_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036325/SRR9036325_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036320/SRR9036320_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036320/SRR9036320_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036360/SRR9036360_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036360/SRR9036360_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036380/SRR9036380_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036380/SRR9036380_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036370/SRR9036370_2_Chimeric.out.junction
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/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036375/SRR9036375_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036375/SRR9036375_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036377/SRR9036377_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036377/SRR9036377_1_Chimeric.out.junction
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/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036373/SRR9036373_2_Chimeric.out.junction
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/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036362/SRR9036362_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036362/SRR9036362_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036311/SRR9036311_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036311/SRR9036311_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036339/SRR9036339_2_Chimeric.out.junction
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/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036349/SRR9036349_1_Chimeric.out.junction
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/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036357/SRR9036357_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036357/SRR9036357_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036381/SRR9036381_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036381/SRR9036381_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036335/SRR9036335_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036335/SRR9036335_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036383/SRR9036383_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036383/SRR9036383_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036327/SRR9036327_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036327/SRR9036327_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036372/SRR9036372_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036372/SRR9036372_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036355/SRR9036355_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036355/SRR9036355_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036317/SRR9036317_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036317/SRR9036317_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036328/SRR9036328_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036328/SRR9036328_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036314/SRR9036314_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036314/SRR9036314_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036324/SRR9036324_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036324/SRR9036324_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036332/SRR9036332_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036332/SRR9036332_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036319/SRR9036319_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036319/SRR9036319_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036331/SRR9036331_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036331/SRR9036331_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036361/SRR9036361_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036361/SRR9036361_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036338/SRR9036338_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036338/SRR9036338_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036310/SRR9036310_2_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample/SRR9036310/SRR9036310_1_Chimeric.out.junction

Here is my directory for sample sheet, I put SRR related STAR results into the specific SRR directory:

Screenshot 2021-12-01 at 17 07 48

Here is my meta1 file: meta2 file is simliar to meta1 file

(circtools-detect) [c.c2050857@cl2 Results]$ cat meta1
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036347/SRR9036347_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036334/SRR9036334_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036315/SRR9036315_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036367/SRR9036367_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036365/SRR9036365_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036371/SRR9036371_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036350/SRR9036350_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036336/SRR9036336_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036326/SRR9036326_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036337/SRR9036337_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036354/SRR9036354_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036368/SRR9036368_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036344/SRR9036344_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036364/SRR9036364_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036342/SRR9036342_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036329/SRR9036329_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036363/SRR9036363_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036307/SRR9036307_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036356/SRR9036356_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036312/SRR9036312_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036353/SRR9036353_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036382/SRR9036382_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036321/SRR9036321_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036374/SRR9036374_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036348/SRR9036348_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036346/SRR9036346_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036309/SRR9036309_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036308/SRR9036308_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036352/SRR9036352_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036318/SRR9036318_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036340/SRR9036340_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036376/SRR9036376_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036343/SRR9036343_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036366/SRR9036366_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036384/SRR9036384_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036359/SRR9036359_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036333/SRR9036333_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036325/SRR9036325_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036320/SRR9036320_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036360/SRR9036360_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036380/SRR9036380_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036370/SRR9036370_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036375/SRR9036375_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036377/SRR9036377_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036322/SRR9036322_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036373/SRR9036373_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036362/SRR9036362_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036311/SRR9036311_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036339/SRR9036339_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036378/SRR9036378_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036358/SRR9036358_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036330/SRR9036330_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036379/SRR9036379_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036369/SRR9036369_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036349/SRR9036349_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036341/SRR9036341_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036313/SRR9036313_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036345/SRR9036345_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036351/SRR9036351_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036323/SRR9036323_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036316/SRR9036316_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036357/SRR9036357_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036381/SRR9036381_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036335/SRR9036335_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036383/SRR9036383_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036327/SRR9036327_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036372/SRR9036372_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036355/SRR9036355_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036317/SRR9036317_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036328/SRR9036328_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036314/SRR9036314_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036324/SRR9036324_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036332/SRR9036332_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036319/SRR9036319_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036331/SRR9036331_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036361/SRR9036361_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036338/SRR9036338_1_Chimeric.out.junction
/scratch/c.c2050857/NAFLD/GSE130970/Results/data/sample_1/SRR9036310/SRR9036310_1_Chimeric.out.junction

Here is my directory for meta1, I put SRR_1 related STAR results into the specific SRR directory:

Screenshot 2021-12-01 at 17 14 18

For example, here is my STAR output, I put all results together.

Screenshot 2021-12-01 at 17 00 57

So now what should I do? Could you please give me a simple example? Do I need to put SRR related STAR results into a specific SRR directory?

Let me know if you need any further information. Thanks!

Birong