bioinfo-biols CIRIquant issues

bioinfo-biols / CIRIquant

circular RNA quantification tools

https://sourceforge.net/projects/ciri/files/CIRIquant

MIT License

27 stars 18 forks source link

issues

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Some questions about the results of ciriquant

#72 mysolid23 opened 1 week ago
0
Add support for single end data and switch to python3

#71 nictru opened 1 month ago
2
I used the parameter --bed with circAtlas bed file, the outputs are always "KeyError: '[circAtlas ID]'"

#70 DooYal opened 1 month ago
3
install CIRIquant using the recommend way

#69 mysolid23 opened 3 months ago
0
Bump scikit-learn from 0.20.3 to 1.5.0

#68 dependabot[bot] opened 3 months ago
0
invalid syntax in hisat2_read_statistics.py

#67 qj009 opened 3 months ago
0
HISAT2 is not working as expected

#66 guillepl opened 5 months ago
0
hisat2-build index for circRNA-seq

#65 fengweimin-maker opened 6 months ago
3
HISAT2 Error: Encountered internal HISAT2 exception (#1）

#64 EdWardYF7 opened 6 months ago
1
Hisat2 produces empty bam files

#63 Braulium opened 7 months ago
0
How to get the p-value from DE analysis?

#62 Li-Chengyu opened 9 months ago
0
sample_index does not exist Exiting now

#61 Yonglee1 opened 10 months ago
3
Question: Predict circRNAs using multiple tools

#60 farzamani closed 10 months ago
1
Issue with EdgeR Installation in CIRIquant

#59 gkibt closed 10 months ago
11
KeyError

#58 stefanerb89 closed 1 year ago
0
CIRIquant for stranded paired-end reads(dUTP method)

#57 junjunlab opened 1 year ago
1
Bump scipy from 1.2.2 to 1.10.0

#56 dependabot[bot] closed 10 months ago
1
Error in prepDE.py

#55 chickenHyop closed 1 year ago
4
Alignment does not end

#54 kendaida closed 1 year ago
0
full-length sequence of circRNA

#53 Zheng19w opened 1 year ago
3
multiple fastq files

#52 sung opened 1 year ago
1
Limitation on Number of Samples Used/DE Filtering Issue?

#51 mlvanhorn opened 1 year ago
1
Error while running CIRIquant

#50 nandakumaryellapu opened 1 year ago
7
A question about the results of differential expression analysis

#49 abedkurdi opened 1 year ago
0
ValueError: file header is empty (mode='rb') - is it SAM/BAM format?

#48 choijamtsmunkhzul closed 1 year ago
0
Problem with installation of CIRIquant

#47 choijamtsmunkhzul closed 1 year ago
0
Small gtf file issue

#46 Mathan98 opened 1 year ago
0
Deferentially expressed circRNAs with biological replicate

#45 ravisaroch closed 1 year ago
1
`os.chmod` error in containers

#44 BarryDigby closed 1 year ago
4
How to measure whether circRNAs are significantly different

#43 litao1503 opened 2 years ago
0
IOError: [Errno 2] No such file or directory: '/mnt/f/liu-project/lncRNA-mRNA-circRNA/5.circRNA-data/quant-data/circ/test.ciri'

#42 junjunlab opened 2 years ago
1
Can CIRI_DE_replicate be used for Differential expression analysis of DS_score

#41 tjhwangxiong opened 2 years ago
3
Error in 'Detecting FSJ reads from genome alignment file'

#40 stefanerb89 opened 2 years ago
2
Bump numpy from 1.16.4 to 1.22.0

#39 dependabot[bot] closed 2 years ago
0
.log show successful completion, but there is no file

#38 algaebrown opened 2 years ago
3
Cannot split into 12 (16) pieces with size of 6246233965 and named them as /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-noD-R_unmapped.sam. Fatal error. Aborted.

#37 algaebrown closed 2 years ago
2
change the permissions on 'CIRI2.pl' while running CIRIquant on cluster

#36 MaryamLabaf opened 2 years ago
3
.fa is empty, index does not exist

#35 algaebrown opened 2 years ago
4
Very low numbers for circular RNAs

#34 FerallOut opened 2 years ago
3
About CircAtlas sequence length

#33 andre-gabriel-42 opened 2 years ago
4
Issue running prepDE.py

#32 G-Molano-LA opened 3 years ago
3
Encountered internal HISAT2 exception (#1)

#31 cjs0617 closed 3 years ago
8
Issue with using find_circ prediction results for CIRIquant

#30 prisca399 opened 3 years ago
1
Generate empty gtf file

#29 mrb20045 closed 3 years ago
10
About BSJs and FSJs

#28 andre-gabriel-42 closed 3 years ago
2
Bump pyyaml from 5.1.1 to 5.4

#27 dependabot[bot] closed 3 years ago
0
EdgeR in CIRI_DE_replicate issue

#26 andre-gabriel-42 closed 3 years ago
7
duplicate rows R error in CIRI_DE_replicate

#25 eltonjrv closed 3 years ago
5
Not able to generate the final circ.gtf output

#24 eltonjrv closed 3 years ago
4
Rowname error with CIRI_DE_replicate command

#23 prisca399 closed 3 years ago
2