Entering edit mode
7.8 years ago
dec986
▴
370
Hello,
I am writing my own GTF file, and featureCounts will only process some of the reads and not others, I have no idea why, as far as I can tell, the lines are identical.
why does featureCounts recognize lines like
chrM ENSEMBL gene 15356 15422 . - . gene_id "ENSMUSG00000064372.1"; gene_type "Mt_tRNA"; gene_status "KNOWN"; gene_name "mt-Tp"; level 3;
chrM ENSEMBL transcript 15356 15422 . - . gene_id "ENSMUSG00000064372.1"; transcript_id "ENSMUST00000082423.1"; gene_type "Mt_tRNA"; gene_status "KNOWN"; gene_name "mt-Tp"; transcript_type "Mt_tRNA"; transcript_status "KNOWN"; transcript_name "mt-Tp-201"; level 3; tag "basic"; transcript_support_level "NA";
chrM ENSEMBL exon 15356 15422 . - . gene_id "ENSMUSG00000064372.1"; transcript_id "ENSMUST00000082423.1"; gene_type "Mt_tRNA"; gene_status "KNOWN"; gene_name "mt-Tp"; transcript_type "Mt_tRNA"; transcript_status "KNOWN"; transcript_name "mt-Tp-201"; exon_number 1; exon_id "ENSMUSE00000521550.1"; level 3; tag "basic"; transcript_support_level "NA";
but not read my added lines, written like this?
chr1 ENSEMBL transcript 13139159 13142763 . - . gene_id "Unknown7"; transcript_id "Unknown7"; gene_type "TEC"; gene_status "PUTATIVE"; gene_name "Unknown7"; transcript_type "TEC"; transcript_status "PUTATIVE"; transcript_name "Unknown7"; exon_number 1; exon_id "Unknown7"; level 3;
chr1 ENSEMBL transcript 13139159 13142763 . - . gene_id "Unknown8"; transcript_id "Unknown8"; gene_type "TEC"; gene_status "PUTATIVE"; gene_name "Unknown8"; transcript_type "TEC"; transcript_status "PUTATIVE"; transcript_name "Unknown8"; exon_number 1; exon_id "Unknown8"; level 3;
chr1 ENSEMBL transcript 13139159 13142763 . - . gene_id "Unknown9"; transcript_id "Unknown9"; gene_type "TEC"; gene_status "PUTATIVE"; gene_name "Unknown9"; transcript_type "TEC"; transcript_status "PUTATIVE"; transcript_name "Unknown9"; exon_number 1; exon_id "Unknown9"; level 3;
I realize this is a tedious question... but I've spent hours on this and I can't see the problem :(
Could you add the command you use for featurecounts with these gtf files?
the command I use is:
Default behavior is to count only for feature 'exon', you have to specify the -t flag, in your case
yes! this solves my problem, instead of using -g.