search

laurahspencer / DuMOAR

0 stars 0 forks source link

Align RNASeq samples to genome using STAR for diff. expression analysis #32

Closed laurahspencer closed 1 year ago

laurahspencer commented 1 year ago

When you're done @ggoetznoaa can you drop your script and the resulting gene count matrix into this repo? Also please provide/confirm which annotation file you used. Thanks!

ggoetznoaa commented 1 year ago

@laurahspencer Ok, I've finished running STAR again against the reference using the GENSAS annotation. I kept the gene counts and I used the default settings. Is there are particular folder you want me to put the gene count matrix file and script I used for aligning?

Also to answer your question, here is what I used for the STAR alignment reference fasta file PGA_assembly.scaffolds_only.fasta

annnotation file Metacarcinus-magister-v1.0.a1.6448195bde6ca-publish.genes.scaffolds_only.gtf

laurahspencer commented 1 year ago

Great! Yes, you can upload the gene count matrix here: https://github.com/laurahspencer/DuMOAR/tree/main/results/STAR

Also, could you add your STAR script here: https://github.com/laurahspencer/DuMOAR/tree/main/scripts

ggoetznoaa commented 1 year ago

Uploaded. I added some comments to the commits as well. Let me know if you need something else or have questions.