<@U03SLE7RBAS> <@UNCU4LKJM> Would be great to get ...
# riboseqj
Jack Tierney
04/29/2025, 11:47 AM@Jonathan Manning @Felix Krueger Would be great to get some thoughts on the params for sortMeRNA that I suggest in this message. This is also relevant to #CE8SSJV3N I think
j
Jonathan Manning
04/29/2025, 11:50 AMI'm not familiar with the option, could you give me a primer? Wouldn't it just take the first alignments, even if suboptimal?
j
Jack Tierney
04/29/2025, 11:53 AMYeah neither am I but I was wondering why we would be running into OOM issues and based on the documentation that comes from storing all alignments in order to find the best. The logic is if we dont look for best (indeed we do not care) we will still find the contaminating rRNA reads just not their exact mappings against the rRNA.
Jack Tierney
04/29/2025, 11:54 AMOr even we would get exact mapping just not necessarily the best mapping. If we got any good hit against rRNA the read can be considered rRNA
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Felix Krueger
04/29/2025, 11:55 AMthat sounds very reasonable
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j
Jack Tierney
04/29/2025, 11:56 AMOkay I will start with a #C05785S3TMX PR and if that gets merged successfully I can create an issue for the #CE8SSJV3N team to decide
j
Jonathan Manning
04/29/2025, 11:57 AMThis will probably have to me a modules PR first
j
Jack Tierney
04/29/2025, 12:02 PMIs it not just a change to args? I might need to look closer. But of course, I can do that if needed
j
Jonathan Manning
04/29/2025, 12:03 PMAhh yes, might just be a config change, you're right
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