Why Read Count is zero, but Covered Bases is not zero?

[jiaojiaoguan]

Hi developer,

Thanks so much for your tool. When I use this cutoff to calculate the abundance, I am curious about the output. Here is the cutoff setting:

--min-read-aligned-percent 90 --min-read-percent-identity 95 --min-covered-fraction 0 --methods rpkm covered_bases length variance count reads_per_base -t 56

Here is the output:
Contig RPKM Covered Bases Length Variance Read Count Reads per base
CSM5FZ3T_P_contigs45 0 35 20515 0 0 0

The number of the read count; reads per base are zero, which means there are no reads aligned with the contigs, but why are the covered bases 35? You may have noticed that I set the --min-covered-fraction 0, so if I want to calculate the covered fraction manually, can I use the covered base/ length?

Looking forward to your reply!

Best,
jiaojiao

[wwood]

Hi @jiaojiaoguan

That's a strange one indeed. Would you be able to run / reproduce by using --bam-file-cache-dir and then samtools view out the matching reads, and then send that please? It is a bit hard to debug otherwise.

Thanks, ben