retroseq.pl line 158.rence file

tk2 / RetroSeq

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.

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retroseq.pl line 158.rence file #6

Open tito3000 opened 8 years ago

tito3000 commented 8 years ago

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: A tool for discovery and genotyping of transposable elements from short read alignments

Version: 1.41 Author: Thomas Keane (thomas.keane@sanger.ac.uk)

Reading -eref file: ereff.tab at retroseq.pl line 158.rence file: rider.fasta

Can you help me please?

file input.zip

tk2 commented 8 years ago

Hi - can you grab the latest release that I just made and try it. That should solve the problem. Let me know if not.

Thomas