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Hey all,
Any advice on this method would be fabulous, I'm new to this and have no programming experience.
I'm trying to compare 4 biological reps of 2 or 3 conditions that I have mapped by Tophat in Galaxy, and because Cuffdiff is not really set up for these types of replicates I am looking at using DEGseq in R instead.
However, I'm not familiar with R and it looks like I need to use BED files for R? I am unable to figure out how to change the BAM files from Tophat to BED files and then use them in the DEGseq command line.
Any tips/help/knowledge would be truly appreciated!
Any advice on this method would be fabulous, I'm new to this and have no programming experience.
I'm trying to compare 4 biological reps of 2 or 3 conditions that I have mapped by Tophat in Galaxy, and because Cuffdiff is not really set up for these types of replicates I am looking at using DEGseq in R instead.
However, I'm not familiar with R and it looks like I need to use BED files for R? I am unable to figure out how to change the BAM files from Tophat to BED files and then use them in the DEGseq command line.
Any tips/help/knowledge would be truly appreciated!