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CIRCexplorer2 parse #61

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muhammadharoon786 opened this issue Jun 20, 2022 · 0 comments
Open

CIRCexplorer2 parse #61

muhammadharoon786 opened this issue Jun 20, 2022 · 0 comments

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@muhammadharoon786
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I wanted to run the parse module. I have used the same command as suggested by manual (CIRCexplorer2 parse --pe -t TopHat-Fusion tophat_fusion/accepted_hits.bam > CIRCexplorer2_parse.log).
However, my log file is not being opened. I want to check it has any kind of error? Further when I submitted the job to cluster, it didnt show the job id. And how could I know its parsing has been completed if I can not open the log file. I used Tophat/2..1.0 version for the alignment. is it necessary to load the tophat module for the parsing step?
used command:
bsub CIRCexplorer2 parse --pe -t TopHat accepted_hits.bam > CIRCexplorer2_parse.log

my bam file was 3.8 gb but the bed file which produced in parsing step is only 17 mb.

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