I am trying to analyse the small RNA sequencing data for Bombyx mori. I have used the ASM15162v1 version of genome as reference. Also, I wanted to count the features of all mapped reads by using the gff file provided for the same available at Ensembl Using htseq or featureCount I am unable to count. It shows an error saying it is a non-standard gff file. I have pasted the three line example of the gff file below. It is indeed not like the standard gtf available for humans.
NW_004581272.1 BestRefSeq exon 5598 5608 . - . ID=id5;Parent=rna0;Dbxref=GeneID:100141452,Genbank:NM_001114933.1;Note=The RefSeq transcript has 3 frameshifts and aligns at 7%25 coverage compared to this genomic sequence;end_range=5608,.;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=Titin1;inference=similar to RNA sequence%2C mRNA (same species):RefSeq:NM_001114933.1;partial=true;product=Titin-like protein;transcript_id=NM_001114933.1
NW_004581272.1 BestRefSeq exon 5568 5595 . - . ID=id6;Parent=rna0;Dbxref=GeneID:100141452,Genbank:NM_001114933.1;Note=The RefSeq transcript has 3 frameshifts and aligns at 7%25 coverage compared to this genomic sequence;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=Titin1;inference=similar to RNA sequence%2C mRNA (same species):RefSeq:NM_001114933.1;partial=true;product=Titin-like protein;transcript_id=NM_001114933.1
NW_004581272.1 BestRefSeq exon 4884 5565 . - . ID=id7;Parent=rna0;Dbxref=GeneID:100141452,Genbank:NM_001114933.1;Note=The RefSeq transcript has 3 frameshifts and aligns at 7%25 coverage compared to this genomic sequence;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=Titin1;inference= similar to RNA sequence%2C mRNA (same species):RefSeq:NM_001114933.1;partial=true;product=Titin-like protein;transcript_id=NM_001114933.1
Are there any tools to convert the above gff format to the one such as human gtf?
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written
by
Sandeep
2 answers
Hi Sandeep,
the file you have is gff3 format and htscount seems to expect gff2 format (gtf is pretty much gff2). I'm surprised it wouldn't work with gff3, either it requires some annotation field or fails on the header?
Anyway, you might try gffread to convert between the formats, but be aware that gff2/gtf can be dangerous to your health ;-)
you might be able to transfer the gene_id from CDS to exons (or convert the parent attribute to gene_id). This is one of the ugly conversion limitations. Btw, the problem with GFF files is almost always the 9th column - this is where the specs get really "flexible"
You can download it from ensembl ftp , the link is here
Additionally, please share the exact command for counting features and the exact error message!
thanks, I didn't know they still maintain a gtf section...
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The command for htseq i use is
htseq-count -m intersection-nonempty -q -t exon -s no PsC.bam ASM15162v1.gffWhich throws an error messagefeatureCount also throws a warning message