10 Meeting notes

This is overall them of the day

How to instruct them to be good RNAseq user?

have a url with multiqc page ready?

This is

explain reference file (FASTA) and annotation files (GTF)

This if you can set up ftp link so that users can pont and click through directory structure to interact with the sikRun output.

Mentione salmon

Good to mention in parsing - salmon if you are using salmon you not going to see DNA contamination. so something to be aware.

Also mentione that this is for model organism that are well annotation/assembled.

Use Chiara’s data to study chromosome 21. From multiqc report chromosome 21 has a lot more reads. It looks like ribosomal contamination even though library was polyA pooled.

Take all reads from chr21 and do feature counts and look where reads go. Suspecting that reads go to ribosomal genes. If so this would be great case study for the workshop.

https://www.ncbi.nlm.nih.gov/pubmed/29788454

genotify

Reproducible research using the same reference files

TCGA for example is using a single reference for the whole cohort

If you gonna do second study e.g chipSeq you gotta have it on the same reference as your RNAseq

there is no such thing as “the reference genome” there are different builds, it is work in progress