Wednesday, November 8, 2017

jax yeast RNAseq module

Because of the waiting of Galaxy job runs, I ask students to work as groups.

One student download all the files to her laptop.

I spent 45 minutes just to have all students retrieve RNAseq data files to their galaxy account.

TopHat is retired at Galaxy.

HISAT2 can be run.
The bam output of HISAT2 can be viewed by UCSC browser directly.

I then use CuffLinks on the aligned bam file to estimate transcripts.

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