CYZbasebio
commented
7 years ago when I give FUCHS a created fold "/DataProcess/Project/qindanProject/Arabidopsis_thaliana/circular_RNA/test20170412_FUCHS/demoOUT/HCOA1" (set -N HCOA1 -O demoOUT), FUCHS seems found what it want and run forward. A new error found:
Traceback (most recent call last):
File "/usr/local/bin/FUCHS", line 11, in
bedtools coverage -split -d -b /DataProcess/Project/qindanProject/Arabidopsis_thaliana/circular_RNA/test20170412_FUCHS/demoOUT/HCOA1/1_24301628_24302463_4reads.sorted.bam -a /home/yuanzhi/tmp/pybedtools.i6GLrN.tmpError message was: Unexpected file format. Please use tab-delimited BED, GFF, or VCF. Perhaps you have non-integer starts or ends at line 1?
FranziMe
Hi，
I found some issues here：
when set -N HCOA1_new， there is a new directory named “HCOA1_new” created in output fold (many bam files and bai files in this fold)， BUT FUCHS will get a error like this:
I guess FUCHS want say "/DataProcess/Project/qindanProject/Arabidopsis_thaliana/circular_RNA/test20170412_FUCHS/HCOA1_new"。
FUCHS option “-s” means SKIPPED_STEPS， but in manual，it means "character used to separate name and exon number".
what the Annotation.bed file should be? what's the difference between "refseq" and "ensembl" specify by option -p, how -e control FUCHS get what it want. I do suggest authors write a real detailed and reproducible workflow for FUCHS, thanks a lot.
here is my command used： FUCHS -r 2 -q 2 -p ensembl -e 2 -T ~/tmp -D CircRNACount -J HCOA1.Chimeric.out.junction -F HCOA1.mate1.Chimeric.out.junction -R HCOA1.mate2.Chimeric.out.junction.fixed -B merged_HCOA1.sorted.bam -A Arabidopsis_thaliana.refseq2.bed -N HCOA1_new
here is annotation.bed used: 1 3630 3913 AT1G01010.1_exon_1_0_1_3631_f 0 + 1 3995 4276 AT1G01010.1_exon_2_0_1_3996_f 0 + 1 4485 4605 AT1G01010.1_exon_3_0_1_4486_f 0 +