Read count using htseq-count.

Question

[Saeed]

Hi

I was trying to load .bam file (Star output) to do read count using htseq-count.

I get this error.

Error occured when processing GFF file (line 3012 of file /ref_genome/stre.gff):
  Feature rna-SCOt01 does not contain a 'gene_name' attribute
  [Exception type: ValueError, raised in count.py:76]

this is a my gff file

##gff-version 3
#!gff-spec-version 1.21
#!processor NCBI annotwriter
#!genome-build ASM20383v1
#!genome-build-accession NCBI_Assembly:GCF_000203835.1
##sequence-region NC_003888.3 1 8667507
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=100226
NC_003888.3     RefSeq  region  1       8667507 .       +       .       ID=NC_003888.3:1..8667507;Dbxref=taxon:100226;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;old-name=Streptomyces coelicolor;serovar=A3(2)
NC_003888.3     RefSeq  sequence_feature        1       21653   .       +       .       ID=id-NC_003888.3:1..21653;Note=TIR-L. Left hand chromosome end terminal inveretd repeat.;gbkey=misc_feature
NC_003888.3     RefSeq  region  435     440     .       +       .       ID=id-NC_003888.3:435..440;gbkey=RBS
NC_003888.3     RefSeq  gene    446     1123    .       +       .       ID=gene-SCO0001;Dbxref=GeneID:1095448;Name=SCO0001;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=SCEND.02c;locus_tag=SCO0001
NC_003888.3     RefSeq  CDS     446     1123    .       +       0       ID=cds-NP_624362.1;Parent=gene-SCO0001;Dbxref=Genbank:NP_624362.1,GeneID:1095448;Name=NP_624362.1;Note=SCEND.02c%2C unknown%2C doubtful CDS%2C len: 225aa;gbkey=CDS;locus_tag=SCO0001;product=hypothetical protein;protein_id=NP_624362.1;transl_table=11
NC_003888.3     RefSeq  region  1238    1243    .       +       .       ID=id-NC_003888.3:1238..1243;gbkey=RBS
NC_003888.3     RefSeq  gene    1252    3813    .       +       .       ID=gene-SCO0002;Dbxref=GeneID:1095447;Name=SCO0002;gbkey=Gene;gene_biotype=protein_coding;gene_synonym=SC8E7.42c,SCEND.01c,SCJ24.01

[jordi.planells]

looks like you don't have "gene_name" in your gff file. If you look closer, you actually have it written as "Name". You can modify the attribute htseq-count is pointing to with -i flag. See the manual

[Saeed]

I am sorry, I tried with "Name" but still not working, "locus_tag" works but gives zero count.

tput_basename.counts SCOr01 0 SCOr02 0 SCOr03 0 SCOr04 0 SCOr05 0 SCOr06 0 SCOr07 0 SCOr08 0 SCOr09 0 SCOr10 0 Any help is appreciated.

[jordi.planells]

Try with ID then, it is a problem of the attribute not being recognized

[Saeed]

I tried it, it doesn't work!

[GenoMax]

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