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

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tmp_DCC files didn't get combine to generate 4 output files #64

Open sambhav2mishra opened 5 years ago

sambhav2mishra commented 5 years ago

Describe the bug tmp_DCC files didn't get combine to generate 4 output files i.e CircRNAcount, CircCoordinates, CircSkipJunctions and LinearCount

Command line used for the command

circtools detect @samplesheet -mt1 @mate1 -mt2 @mate2 -D -R Final_repeats.gtf -an gencode.v30.annotation.gtf -Pi -F -M -Nr 5 6 -fg -G -A GRCh38_gencode.fa

Complete error message

Screenshots detect Files _in_dir_to_run_detect

Desktop (please complete the following information):

OS: [ Ubuntu 18.04]
Python version [Python 2.7.15rc1]

tjakobi commented 5 years ago

Hi @sambhav2mishra ,

did you try to set the filtering threshold lower, i.e. -Nr 2 2 for example? The warning message just states that no circles have been found which is most probably due to to stringent filtering.

Cheers, Tobias

sambhav2mishra commented 5 years ago

Thanks Tobias it helped me with filtering but it gave another problem:

File "/home/dranshuman/.local/bin/DCC", line 11, in load_entry_point('DCC==0.4.7', 'console_scripts', 'DCC')() File "build/bdist.linux-x86_64/egg/DCC/main.py", line 364, in main File "build/bdist.linux-x86_64/egg/DCC/circFilter.py", line 92, in filter_nonrep File "build/bdist.linux-x86_64/egg/DCC/circFilter.py", line 85, in read_rep_region File "/home/dranshuman/.local/lib/python2.7/site-packages/HTSeq-0.11.2-py2.7-linux-x86_64.egg/HTSeq/init.py", line 207, in iter strand, frame, attributeStr) = line.split("\t", 8) ValueError: need more than 1 value to unpack

tjakobi commented 5 years ago

Hi @sambhav2mishra,

could you please paste the first lines of your repeat annotation file?

head Final_repeats.gtf

Cheers, Tobias

sambhav2mishra commented 5 years ago

Hello Tobias although you recommended to choose RepeatMasker together with Simple Repeats and combine the results afterwards but i have created my gtf file using only repeatMasker and i have attached a file consisting of few lines of annotation file. gtf.txt