cds cd my_rnaseq_course cp -r /corral-repl/utexas/BioITeam/rnaseq_course/exercises . cd exercises
A) We have the fastq file, test.fastq. Can you find out how many reads we have in this fastq file? Can you think of multiple ways to do this?
B) The instructions asked you to copy the directory exercises. But I left out one file. Can you copy that over to your exercises directory? You'll need to view it because it has your next exercise.
The file is at
/corral-repl/utexas/BioITeam/rnaseq_course/C
C) See above
D) We are concerned that a weird artifact sequence may be in our data- ACTACCGATCCA Can you find out what proportion of our reads have this artifact?
E) We want to trim this sequence out from our data? Can you do that?
F) Ok we’ve mapped the data using top hat. We have a bam file (test.bam) and annotation file (genes.gtf) and want to assemble novel and annotated transcripts using cufflinks. Can you submit a cufflinks job that to lonestar? Of course we are not utilizing lonestar fully because we are just submitting one job, but this is for practice.
G) Ok we've assembled transcripts etc and run cuffdiff to get differential gene expression information.