Hello,
Does anyone know where I can download a GTF file that will work using Tophat and their provided mm9 build? I downloaded the version from ftp://ftp.ensembl.org/pub/current/gtf/mus_musculus/ and keep getting the following error:
[Thu Oct 28 12:08:01 2010] Reading known junctions from GFF file
Warning: TopHat did not find any junctions in GFF file
I have even tried reformatting the file by adding "chr" in front of everything in the first column of each line (this changes the notation of X of 18 to chrX or chr18). At this point I would prefer downloading a GTF build that works with Tophat v1.1.1 but I can also try to modify the file I have now if someone knows what needs to be changed
A sample of one line of the GTF file:
18 protein_coding CDS 30483176 30483260 . + 0 gene_id "ENSMUSG00000033628"; transcript_id "ENSMUST00000115811"; exon_number "20"; gene_name "Pik3c3"; transcript_name "Pik3c3-004"; protein_id "ENSMUSP00000111478";
-Keith
Does anyone know where I can download a GTF file that will work using Tophat and their provided mm9 build? I downloaded the version from ftp://ftp.ensembl.org/pub/current/gtf/mus_musculus/ and keep getting the following error:
[Thu Oct 28 12:08:01 2010] Reading known junctions from GFF file
Warning: TopHat did not find any junctions in GFF file
I have even tried reformatting the file by adding "chr" in front of everything in the first column of each line (this changes the notation of X of 18 to chrX or chr18). At this point I would prefer downloading a GTF build that works with Tophat v1.1.1 but I can also try to modify the file I have now if someone knows what needs to be changed
A sample of one line of the GTF file:
18 protein_coding CDS 30483176 30483260 . + 0 gene_id "ENSMUSG00000033628"; transcript_id "ENSMUST00000115811"; exon_number "20"; gene_name "Pik3c3"; transcript_name "Pik3c3-004"; protein_id "ENSMUSP00000111478";
-Keith
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