Closed drivenbyentropy closed 9 months ago
Hi @drivenbyentropy - this is mainly caused by read splitting in dorado. The parent read id of the split read will correspond to the original entry in the pod5. Here's some info on split read specific tags - https://github.com/nanoporetech/dorado/blob/master/documentation/SAM.md#split-read-tags
@tijyojwad Thank you very much for your prompt answer, this is exactly what I was missing. I encountered this issue when working with the remora API which appears not to support split read input and calls can_pod5_fh.reads()
with missing_ok=False
hence failing if any of the bam reads were split. I will open a separate ticket over there for this issue.
Thank you very much again for pointing me towards the solution!
Hello,
I am facing a strange issue that I am not able to solve on my own and would appreciate any insight as to what I might be missing here. I have a dataset of reads from a plasmid spiked with other, distinct DNA that was sequenced on a
PromethION P2 Solo
. Relevant details regarding this run are as follows:I am basecalling and aligning the data from a single
pod5
file (no otherpod5
files are present in the same folder or subfolder) to produce a sortedbam
file withdorado v0.4.2
as follows:However, when trying to create pairs of matching
raw reads
andbam reads
, it appears that not all reads present in thebam
file can be found in thepod5
:My expectation would be that the intersection size between the
bam ids
and thepod5 ids
corresponds to the number ofbam ids
. What could I be missing here that could cause such a scenario? Where could the additionalbam ids
be coming from? What approach could I take to debug this issue further?Thank you very much in advance for your advice!