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wdecoster / cramino

A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
MIT License
129 stars 11 forks source link

Report aligned bases #26

Open Shians opened 8 months ago

Shians commented 8 months ago

Would it be possible to report % aligned bases on top of % aligned reads?

wdecoster commented 8 months ago

Not easily, in the current implementation, or not without a lot of overhead. The closest you can currently get is to run with default settings on your aligned bam, and once with --ubam on an unaligned bam. But I agree that is not great. Could you elaborate on why that would be an important metric for you?

Thanks, Wouter

Shians commented 8 months ago

I consider the amount of throughput of a long-read experiment to be the gigabases sequenced rather than number of reads. By extension I think of the proportion of gigabases aligned to be the measure of useful data obtained.