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I am trying out your very nice dynast pipeline (version 0.2.0) I ran into an issue with counting after creating a consensus bam file. Somehow the consensus.bam has lost the gene-tag or gene assignment after completion. Mind you the flag for gene-tag differs from your default value "GX", but I specify --gene-tag GE when running the consensus command. I checked the in and output bam files for the presence of my gene-tag (see below), plus here is the command I ran
Is this normal and one should disregard the --gene-tag for counting after consensus building, or do you have any good input as to why this might have happened?
Thanks in advance.
Best,
Michael
The text was updated successfully, but these errors were encountered:
mhagemann86
changed the title
Consensus.bam lost gene-tag after
Consensus.bam lost gene-tag after completion
Jul 1, 2022
The BAM output from the consensus command should have the gene ID placed in the GX tag and gene name in the GN tag, regardless of what tags were used as input. Would you please check if these tags are present?
Hi,
I am trying out your very nice dynast pipeline (version 0.2.0) I ran into an issue with counting after creating a consensus bam file. Somehow the consensus.bam has lost the gene-tag or gene assignment after completion. Mind you the flag for gene-tag differs from your default value "GX", but I specify --gene-tag GE when running the consensus command. I checked the in and output bam files for the presence of my gene-tag (see below), plus here is the command I ran
Is this normal and one should disregard the --gene-tag for counting after consensus building, or do you have any good input as to why this might have happened?
Thanks in advance.
Best,
Michael
The text was updated successfully, but these errors were encountered: