Retroseq Error For -Reftes Option

Question

[roll]

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 ([e-mail])

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?

Answer 1

[SES]

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.

[roll]

I changed -refTEs argument to a file which contains SINE \t mysine.bed. it is working. do you think including more than one line and type will work? for example SINE in one line and LINE in the second line etc.

[drtkeane]

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.