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two samples with 0% alignment

I have about 12 samples I aligned with mm39. All samples had good quality reads and all paired, as trimmomatic gave me empty files for unpaired reads. Strangely, two of them had 0% alignment with the genome. I blasted a few reads and they seem to match mus musculus or other rodents. I'm using HISAT2 on galaxy. Is it a bug?

galaxy hisat2 rna-seq
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written by demoraesdiogo2017 • demoraesdiogo2017

1 answer

If you are using PSU public galaxy then please post this on their help forum for prompt response: https://help.galaxyproject.org/

That said this could just be failed jobs on galaxy so no harm in re-trying the alignments.

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written by GenoMax GenoMax

I have undeleted the post so that others can see what the right course of action is if they have similar questions.

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written by Istvan Albert Istvan Albert

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