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BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA
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Combined samples and then map or map samples separately? #146

Closed callumparr closed 2 years ago

callumparr commented 3 years ago

Is it expected to combine all the pass FASTQ files from all samples you have and then map with flair.py align or to map separately then combined the .psl files before the next step, flair.py correct ?

I could not see a way to feed in multiple FASTQ for minimap2 that would also output separate SAM files for each sample.

After I annotate splice sites I would like to use this for differential expression analysis so would need to go back to original samples and conditions again.

Jeltje commented 2 years ago

You should run them separately and combine them at the Flair quantify step.

Flair align allows input of multiple fastq files as a convenience, in case you have multiple files per sample. It has no way of keeping track of which reads came from which input file.

Hope this helps!