Comments (1)
Hi @rocpv1977!
Thanks for the question. You're definitely on the right track. You are expected to give it the output from seqkit bam
on a bam file that does not have secondary alignments. If your alignment has been done in a way that includes secondary alignments, you would be expected to filter out secondary reads, for example with samtools view
:
samtools view -F 256 input.bam > nosecondary.bam
seqkit bam nosecondary.bam 2> nosecondary.txt
Excuse the confusing naming and the lack of documentation regarding this. It's worth tidying up.
Best regards
from duplex-tools.
Related Issues (20)
- pairs.txt file empty, but pairs_from_bam/pair_ids.txt not empty HOT 1
- empty output from split_pairs HOT 5
- KeyError: 'sequence_length_template' when basecalling is turned off HOT 2
- Duplicate reads and read splitting option in MinKNOW HOT 9
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- promethion good pairs: 0 HOT 3
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- np.bool deprecated, package no longer works HOT 1
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- merging original duplex bam file with the addtional split duplex bam file HOT 1
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from duplex-tools.