search

Mayrlab / utr-enhancers

QAPA pipeline for enhancer-related RNA-seq datasets
1 stars 0 forks source link

Question about salmon/sample/*quant.sf file in scripts #1

Open NJU-Bio-Info opened 2 years ago

NJU-Bio-Info commented 2 years ago

Hi, when I learn your R scripts about DESeq and DEXSeq, I wonder that the quant.sf file here is the output of qapa?

mfansler commented 2 years ago

Thank you for the question. The .sf file is the output from salmon. For example, the rule salmon_quant_pe will generate this by running the salmon quant command.

I will add a README file in the next days, to describe more in detail how the pipeline is run. Note that what is currently the normalize is what was used in the final analysis. I will eventually move this too main. I'll let you know when I've updated, but free feel to ask any more clarifications!

NJU-Bio-Info commented 2 years ago

Yeah, I really want to learn from your scripts about how to identify different polyA sites usage(or transcript isoform) with the output of QAPA. If you can make some clarification for this topic, you will help me a lot about my project!!! Really want to see your update!

NJU-Bio-Info commented 2 years ago

The index for salmon used to generating .sf file in DEXseq.R and DESeq.R is the output utr sequence(.fa file)? or the whole genome(transcriptome)?

mfansler commented 2 years ago

That's a good question. I'll make sure to include the provenance for that in the write-up.

The index is from the QAPA v1.3.0 release, then using the UCSC mm10 genome as a decoy. The steps to replicate the index are documented in the Snakefile in my mm10-db repository.