I ran I ran Cuffdiff using an ENSEMBL genome (rat RGSC3.4) and want to look at my alignments using IGV
I tried to upload the genome and gtf file I downloaded from ENSEMBL to IGV but it is not working.
If I upload my bam file to IGV using their rn4 (UCSC version of the rat genome) the alignments seem to match up with the genes. Is this kosher or will I run into problem? How compatible are the different genome versions?
Also happy to know if anyone has pros/cons of using one vs the other when doing differential expression analyses
Thanks!
I tried to upload the genome and gtf file I downloaded from ENSEMBL to IGV but it is not working.
If I upload my bam file to IGV using their rn4 (UCSC version of the rat genome) the alignments seem to match up with the genes. Is this kosher or will I run into problem? How compatible are the different genome versions?
Also happy to know if anyone has pros/cons of using one vs the other when doing differential expression analyses
Thanks!
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