Htseq-count: Problem with feature counts

Question

[MolGeek]

Hi all.

I want to perform read count from several bams (Alignment was performed using mm10) using the htseq-count.

I am using the Mus_musculus.GRCm38.101.ccds.gtf:

    head Mus_musculus.GRCm38.101.ccds.gtf 

1   ensembl_havana  exon    3214482 3216968 .   -   .   gene_id "ENSMUSG00000051951"; gene_version "5"; transcript_id "ENSMUST00000070533"; transcript_version "4"; exon_number "3"; gene_name "Xkr4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000026353"; havana_gene_version "2"; transcript_name "Xkr4-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS14803"; havana_transcript "OTTMUST00000065166"; havana_transcript_version "1"; exon_id "ENSMUSE00000448840"; exon_version "2"; tag "basic"; transcript_support_level "1":

The command is:

htseq-count -f bam -t exon File1.bam Mus_musculus.GRCm38.101.ccds.gtf > File1.txt

The output is:

ENSMUSG00000118396  0
ENSMUSG00000118409  0
ENSMUSG00000118459  0  
ENSMUSG00000118506  0
ENSMUSG00000118560  0
__no_feature 30945311 
__ambiguous 0
__too_low_aQual 0 
__not_aligned 6999135 
__alignment_not_unique  7287645 

The code runs without errors but feature counts are 0.

How could i fix it?

[bioinfo_ga]

Along with -t option you also need to provide -i option where you can mention the attribute for which you need the count (e:g exon_id).

[MolGeek]

I already tried but it doesn't work.

Answer 1

[Istvan Albert]

perhaps the chromosome naming differs 1 vs chr1

[MolGeek]

That worked fine. Thank you!