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 (email@example.com) 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?