RetroSeq
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tk2
RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below)...
Hi, I am getting the below error during `Calling` step: `Command: ./bin/retroseq.pl -call -bam /scratch/G300B1.bam -input /scratch/retroseq/sinec -ref /scratch/l1.0_ROSY.fa -output /scratch/retroseq/sinec.vcf -filter SINEC.refTEs.txt -reads 3 -depth 400` Tail of the...
Hi @tk2, Many thanks for maintaining RetroSeq - great tool! After some performance tests, I just realised that the default parameter settings in your retroseq.pl -call raw description are actually...
When I run RetroSeq in the align mode, it gets to PE alignment parsing and then breaks. Not sure what the error means (uninitialized value before assignment?). Input: perl bin/retroseq.pl...
https://github.com/tk2/RetroSeq/blob/9d4f3b5270af2383f40e6e7ea1204ea718365db2/bin/retroseq.pl#L249
when I run the step 2 of Retroseq, the software tell me: Cant find BAM input file or BAM index file here is my whole command: step 1: retroseq.pl -discover...
Hi I ran retroseq.pl and i got the errors : Useless use of greediness modifier '+' in regex; marked by
I have merged .bam files from the 1kGP (with samtools merge -r) and performed RetroSeq discovery phase on the merged .bam. But now when I call the merged .bam I...
Hello! I am working on running through RetroSeq, and it seem that the discover stage is working - but the call stage give me this error, which I haven't been...
Dear all; I'm trying to install and launch RetroSeq (using mac os); When I run the command line: perl retroseq.pl -discover -bam file.bam -out ... I obtain this msg: Error:...
Hi all I'm trying to launch RetroSeq (using ubuntu os). When I run the command line: perl retroseq.pl -discover -eref ereff.tab -bam file_sorted.bam -output mysample.candidates.tab I obtain this msg: RetroSeq:...
