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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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Hisat2, stringtie protocol for paired-end and single reads #142

Open bioinfo17 opened 7 years ago

bioinfo17 commented 7 years ago

Hi,

As per the published hisat2/stringtie protocol, hisat2 is used with paired-end reads. I was wondering if hisat2 can be run using paired-end and singleton/single-read files together using -1, -2 and -U in the same command line? I'm really interested to know if this will have an effect on the counts (generated by the prepDE.py script) if the resulting bam files are used in stringtie for differential expression analysis.

How does stringtie deal with having paired-end and singleton read alignments in the bam files?

Should one ignore the singleton reads and just use the paired-end reads (use only -1, -2 and not -U) or Should one treat all reads as unpaired and use -U R1, R2, singletons to generate count tables using stringtie?

I have read papers and have looked for answers in the forums etc. but haven't received any definitive answer so far so trying my luck here.

Any advise will be much appreciated!!

jtstanley commented 6 years ago

Hey there, did you ever figure out the answer to your question? I'm currently in the same boat, but was having a hard time finding answers in the official hisat2/stringtie documentation.

I'd love to hear what you figured out. Thanks!

Duannai commented 2 years ago

Hello, do you have an answer?

Thanks!