Closed aherman-umn closed 9 months ago
Ah, I've got it, Below min passes
is np:i:0
from the CCS bam + NumPasses 0
from lima
, which is scored based on adapter structure in the read and is only determined for np:i:n
> 0.
samtools view M145_reads.bam | cut -f 12- | tr '\t' '\n' | grep 'np:i:' | sort | uniq -c | sort -k2,2V | head
1745145 np:i:0
362574 np:i:1
263808 np:i:2
234643 np:i:3
200416 np:i:4
173981 np:i:5
156908 np:i:6
142309 np:i:7
130874 np:i:8
121740 np:i:9
So there are 1745145 zero pass CCS reads and if we add the 139 zero pass fl reads from lima we get the Below min passes: 1745284
value. Zero pass CCS reads are counted for the .summary
file but are not included in the .report
file, which is what confused me!
Hi there,
Looking at my lima *.summary output for my IsoSeq data I'm getting a sizable number of reads not passing the minimum pass filter. I was under the impression that the
--min-passes 0
was the default, is that overridden by--isoseq
? I seeFullPass : false
when I runAnd pretty much everything is single pass...
But I've got 1.75M reads getting filtered out?
Any insight is greatly appreciated!