Mixing single-end and paired-end reads in Trinity Genome Guided

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Nicolas Delhomme

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May 21, 2021, 5:44:12 PM5/21/21

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Hej Brian!

I have a bunch of samples sequenced single-end and another set sequenced paired-end. We have just completed a genome assembly and would like to generate transcripts from the RNA-Seq data (hence using the genome-guided approach) to use as evidence for the ab-initio gene annotation. The thing is that some sample types are unique to the single-end sequenced libraries and I was wondering if I could merge the reads into a single BAM. Can trinity handle that or would I be better off running two trinityGG, one per seq type and merging the resulting transcripts?

Best,

Nico

Brian Haas

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May 22, 2021, 7:00:49 AM5/22/21

to Nicolas Delhomme, trinityrnaseq-users

Hi Nico,

If the samples correspond to different tissue types, I'd recommend assembling them separately to avoid chimeric assembly of tissue-specific isoforms. Then, you could merge the transcript sets from the different runs later on.

I haven't tested running Trinity in genome-guided mode with combined single and paired-end reads. If the data are strand-specific, then genome-guided mode isn't configured to work properly with mixed data like this. If it's not strand-specific, then it could be fine, but be sure to give the parameter --run_as_paired to avoid Trinity trying to figure this out by sniffing the bam.

hope this helps!

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