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) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
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 able to figure out which file it is missing?
Found sample: CPBWGS_11
Calling sample CPBWGS_11
Beginning paired-end calling...
PE Call: >rnd-2_family-5LINE/CR1-Zenon(ReconFamilySize=93,FinalMultipleAlignmentSize=88)
No such file or directory at retroseq.pl line 660, <$tfh> line 1.
Hello! I am working on running through RetroSeq, and it seem that the discover stage is working - but the call stage give me this error, which I haven't been able to figure out which file it is missing?
Found sample: CPBWGS_11 Calling sample CPBWGS_11 Beginning paired-end calling... PE Call: >rnd-2_family-5LINE/CR1-Zenon(ReconFamilySize=93,FinalMultipleAlignmentSize=88) No such file or directory at retroseq.pl line 660, <$tfh> line 1.
Thanks! Kristian