Error at parsing .tlst line (invalid strand): 3210 PGSC0003DMT400030180 ST4.03ch12. 56298573-56298656

Question

[Pac314]

Hi, I am new to RNA-seq and am trying to map paired-end reads with TopHat but I keep getting this error:

    [2021-11-15 19:37:57] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2021-11-15 19:37:57] Checking for Bowtie
          Bowtie version:    2.4.4.0
[2021-11-15 19:37:58] Checking for Bowtie index files (transcriptome)..
[2021-11-15 19:37:58] Checking for Bowtie index files (genome)..
[2021-11-15 19:37:58] Checking for reference FASTA file
[2021-11-15 19:37:58] Generating SAM header for ~/data/potato_chr12
[2021-11-15 19:37:59] Reading known junctions from GTF file
[2021-11-15 19:37:59] Preparing reads
     left reads: min. length=101, max. length=101, 1902638 kept reads (41 discarded)
    right reads: min. length=101, max. length=101, 1902643 kept reads (36 discarded)
[2021-11-15 19:39:10] Using pre-built transcriptome data..
[2021-11-15 19:39:11] Mapping left_kept_reads to transcriptome potato_chr12 with Bowtie2 
    [FAILED]
Error running:
/apps/software/TopHat/2.1.1-foss-2016b/bin/bam2fastx --all tophat_out/tmp/left_kept_reads.bam|/data/bowtie2-2.4.4/bowtie2 -k 60 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 8 --sam-no-hd -x ~/data/potato_chr12.tr/potato_chr12 -|/apps/software/TopHat/2.1.1-foss-2016b/bin/fix_map_ordering --bowtie2-min-score 15 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --sam-header tophat_out/tmp/potato_chr12.bwt.samheader.sam - - tophat_out/tmp/left_kept_reads.m2g_um.bam | /apps/software/TopHat/2.1.1-foss-2016b/bin/map2gtf --sam-header tophat_out/tmp/potato_chr12_genome.bwt.samheader.sam ~/data/potato_chr12.tr/potato_chr12.fa.tlst - tophat_out/tmp/left_kept_reads.m2g.bam > tophat_out/logs/m2g_left_kept_reads.out

I looked at error file and it contains this:

Error at parsing .tlst line (invalid strand):
3210 PGSC0003DMT400030180 ST4.03ch12. 56298573-56298656

This is the only line that has a "." in the after the seqID. Please could you help me fix this issue.

Answer 1

[skbrimer]

Looks like this is a common problem.

This post discusses the issue .gtf file error in Tophat2 - Error at parsing .tlst line (invalid strand):

and this one says you need to filter the input file to remove the "." lines tophat2 GTF invalid strand error

[Pac314]

Thank you for replying and for providing a link to that post. One of the posters in the link you provided said it shouldn't be much of an issue removing the offending line, do you agree with this opinion?

[skbrimer]

I would think since it's empty deleting it should be fine. Might need to remake any index files but that is not hard either. Good luck