HTseq-Count: Long processing time
Hi everyone, I'm processing BAM files using htseq-count and it takes very long time to produce the counts for each file. It is about pair-end reads (around 50 million sequence each). It takes 75 minutes to count this pair; is that normal? Thanks.
htseq-count --max-reads-in-buffer=24000000000 -s no -r pos -t exon -i gene_id -f bam Sample1_Aligned.sortedByCoord.out.bam Homo_sapiens.GRCh38.106.gtf > Sample1-output_basename.counts
1 answer
The original paper stated that on a normal laptop (back in 2015) it can process 600.000 read pairs per minute, which would mean 50M reads (I guess you have 50mio pairs) take 83min, so yes, that's normal. A much faster alternative is featureCounts from the subread package.
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