HTSeq – Extracting exon level read coverage of a specific gene
I am trying to quantify RNASeq reads at the “exon level” using HTSeq. To achieve a quantitative exon comparison.
I am using ENCODE mouse data which is Illumina reads alligned to GENCODE M27 (GRCm39) using STAR (bam files) and a relevant index (bai) file generated by Samtools.
My HTSeq command is as follows:
$htseq-count -f bam -r pos -s no -t exon -i gene_id --additional-attr=gene_name--additional_attr=exon_number Aligned.sortedByCoord.out.bam ~/Gencode_Mouse_39/gencode.vM27.primary_assembly.annotation.gff3 > exon_counts.txt
Apparently this approach provides exon coverage for all “gene_id” attributed genes.
Is there any method to limiting this approach to a “specific” ensemble annotated gene only? (present in the GFF file?)
I have gone through the HTSeq documentation as well as several topics but couldn’t find any example or implementation.
Any comments or suggestions are welcome
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