Closed hasindu2008 closed 3 weeks ago
The latest verison of guppy_barcoder in the dorado_server release apparently fixes the memory leak issue, and may have some other features. we should check that out before I do something in buttery-eel
Yea latest ont_barcoder takes bam as an input
that os good!
Please add the following instructions to somewhere:
For FASTQ output from buttery-eel, we call guppy_barcoder which comes with the ONT Guppy package for demuxing. It seems that guppy_barcoder does not take uSAM as input. However, the following approach that converts uSAM to FASTQ (keeps the methylation information as name tags) can be used for demuxing.
Note that if your remora.mods.fastq file is pretty large and your RAM is less than the size of fastq, Guppy_barcoder will run out of memory as it seem to load the whole fastq file to memory. To avoid this issue,we can split the big fastq file into smaller files as below:
Some versions of Guppy barcoder seem to incorrectly use a space instead of a tab for separating runid and barcode tags, causing issues in downstream processing. So please fix your barcoded FASTQs as below, before using with tools such as Minimap2.