RNA STAR error on Gallaxy

Question

[genya35]

Hello,

Please help to figure out how to fix the following error:

Fatal INPUT FILE error, no valid exon lines in the GTF file: /galaxy-repl/main/files/021/715

I've made fastQ file from Ion Torrent unmapped RNA bam by using samtools bamtofastq and running the file on (RNA-STAR) in Galaxy.

I've downloaded Homo_sapiens.GRCh37.75.gtf from tp://ftp.ensembl.org/pub/ and ran the job.

I got an error message several minutes after starting the job: "Fatal INPUT FILE error, no valid exon lines in the GTF file: /galaxy-repl/main/files/021/715"

I did see a post about removing/changing "chr" in gtf file but it's not clear how and what to do exactly. I would really appreciated if someone could explain how to fix this problem.

I have ran this fastq file on other RNA aligners so it must something to do with GTF file.

Thank you for your help.

Answer 1

[Devon Ryan]

You should post this sort of error on the galaxy site.

The likely cause of this is the chromosome name mismatch you referred to. Given the file path you mentioned I'm guessing you're using the main usegalaxy.org site. That seems to use UCSC chromosome names (e.g., chr1 and chrM), while Ensembl (where you got the GTF file) uses other names (e.g., 1 and MT). You'll want to either add chr to the chromosome column. One possibility would be to use the Text reformatting tool (for the bioinformaticians out there, it's a Galaxy wrapper for awk) with something like the following as the AWK Program:

BEGIN{OFS="\t"}{$1=sprintf("chr%s", $1); print}

Alternatively, download a GTF file from UCSC.