Hi,
I am trying to run the RetoroSeq for the first time. I am at the first stage and keep getting the following error message:
Command I used is:
perl retroseq.pl -discover -bam my.bam -refTEs repeats.bed -output retro_out -q 20
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 -refTEs file: /cluster/project8/RNA_seq_CI/repeats/repeats.bed
Cant find chr2 181585004 181585176 B3 reference TEs file: SINE/B2 at /home/regmtun/softwares/RetroSeq-master/bin/retroseq.pl line 170
couple of lines from repeats.bed looks like this (i downloaded this from UCSC as fa and converted it to bed file):
chr10 3000001 3001868 MMETn-int LTR/ERVK
chr10 3001869 3002170 RLTRETN_Mm LTR/ERVK
chr10 3002335 3002411 MIR SINE/MIR
chr2 181585004 181585176 B3 SINE/B2
Any advice what is going wrong?
1 answer
That message is saying that the program is looking for a file that could not be found (probably SINE.fasta), but that is not the actual issue. From the looks of your command line, I think you are supplying the wrong argument to the -refTEs option. That option should take a two column file (separated by a single tab) of TE types. To be certain, make sure your format is correct in the types file before you use it, and check that SINE/B2 can be found (in that reference types file). If that does not solve the issue, please comment or update your post.
Yes, having multiple different TE types in the -refTEs file will work. In fact this is the intended usage so that you can call multiple different TE insertions in a single run of the program.
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