search

lh3 / minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences
https://lh3.github.io/minimap2
Other
1.77k stars 404 forks source link

minimap2 results to DESEQ2 #401

Closed uhlkatie closed 5 years ago

uhlkatie commented 5 years ago

Does anyone have experience with taking the resulting .sam/.bam files from minimap2 and funneling them into a differential analysis package? Specifically, I am looking to take reads from Direct RNA sequencing on the Oxford Nanopore Technology MinION to something similar to DESeq2. I chose minimap2 because the parameters can be tailored to fit the noisy long-reads from the MinION. I was able to run minimap2 successfully, but from there I have hit a wall. I attempted to follow the document: https://bioc.ism.ac.jp/packages/2.14/bioc/vignettes/DESeq2/inst/doc/beginner.pdf

But when it comes to the sample table, I am confused as to how to find/generate it. Any help or advice for a first time RNA-seq analysis would be greatly appreciated.

lh3 commented 5 years ago

I am afraid you have to ask the DESeq2 developers.

cc @mikelove

mikelove commented 5 years ago

There was a recent thread on the support site:

https://support.bioconductor.org/p/120764/

lh3 commented 5 years ago

Thanks, @mikelove! I am closing the issue here.