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jsh58 / Genrich

Detecting sites of genomic enrichment
MIT License
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Error! 'x': unknown value type in BAM auxiliary field #42

Closed alund1394 closed 4 years ago

alund1394 commented 4 years ago

Hi,

I am using Genrich in ATAC-seq mode for reads aligned with Bowtie2.

(I am using the pipeline described here: https://informatics.fas.harvard.edu/atac-seq-guidelines.html)

I was able to generate a narrowPeak file successfully with one data set, but now I am getting the error 'x': unknown value type in BAM auxiliary field.

Thanks!

jsh58 commented 4 years ago

Thanks for the question. This is an ununusual error, especially with a bowtie2-produced BAM file. According to the SAM spec (Sections 1.5 and 4.2.4), x is definitely not a valid value type.

Let's see if we can extract some of the offending records. Please post the result of this command:

$ samtools view <BAM> | grep -m5 ':x:'