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YangLab / CLEAR

direct comparison of circular and linear RNA expression
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NO quant or circular output #19

Open lbwfff opened 2 years ago

lbwfff commented 2 years ago

I run the software with the following parameters： clear_quant -1 ~/biodata/hcc-ribo/rmrRNA/LC501_tumor_totalRNA.derrRNA.fq.gz -g ~/biodata/index/GRCh38/GRCh38.primary_assembly.genome.fa -i ~/biodata/index/GRCh38/GRCh38 -j ~/biodata/index/GRCh38/GRCh38 -G ~/biodata/annotation/gencode.v35.annotation.sorted.gtf -o ~/tools/CLEAR-master/test2 -p 18 No error was reported during the process, the following is the output log：

###Parameters:
Namespace(bowtie1='/home/leelee/biodata/index/GRCh38/GRCh38', genome='/home/leelee/biodata/index/GRCh38/GRCh38.primary_assembly.genome.fa', gtf='/home/leelee/biodata/annotation/gencode.v35.annotation.sorted.gtf', hisat='/home/leelee/biodata/index/GRCh38/GRCh38', m1='/home/leelee/biodata/hcc-ribo/rmrRNA/LC501_tumor_totalRNA.derrRNA.fq.gz', m2=None, output='/home/leelee/tools/CLEAR-master/test2', thread='18')
###Parameters

###Start hisat2 mapping
# start to get sp sites for hisat mapping
# start to align to genome by hisat
# get mapped and unmapped reads
# sort bam file
# index bam file
###End hisat2 mapping

###Start tophat-fusion mapping
###End tophat-fusion mapping

###Start circRNA annotation
###End circRNA annotation

###Start circRNA quantification
###Parameters:
Namespace(bam='/home/leelee/tools/CLEAR-master/test2/hisat/align.bam', circ='/home/leelee/tools/CLEAR-master/test2/circ/circular.txt', length=False, output='/home/leelee/tools/CLEAR-master/test2/quant/quant.txt', ratio=1, ref='/home/leelee/tools/CLEAR-master/test2/circ/annotation.txt', threshold=1, tmp=True)
###Parameters
###End circRNA quantification

But I found that the size of my circular.txt and quant.txt files are both 0 Bytes, and the accepted_hits.bam file is 65m. I am confused about this. Is this situation because circularRNA is not found in my sequencing file or because the software is running There was an error in a certain step of?

lbwfff commented 2 years ago

Oh, it suddenly occurred to me that I could run the files in test_data, and I got the desired result. It seems that the software did not find circularRNA in my sequencing file.

guillaumecharbonnier commented 1 year ago

This phenomenon also occurred to me because my HISAT index was defined without "chr" while gtf and bowtie one were defined with it. For other mismatched chromosome names, the tool outputs a clear error message but not for this one.