Entering edit mode
14 months ago
Trivas
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1.7k
I've googled and found nearly every thread on this topic on Biostars and it seems like the consensus to visualizing stranded RNA-seq data is splitting your BAM file into one for each strand. I'm dealing with a lot of different BAM files and would rather not double my file number.
I followed this blog https://www.r-bloggers.com/2014/11/visualising-stranded-rna-seq-data-with-gvizbioconductor/ and got it to work one day and then the very next it stopped working saying Error in .legendInfo()[type, , drop = FALSE] : subscript out of bounds.
Honestly willing to try anything - I can convert to any file format, I will learn any R package, as long as I can use a custom genome and custom gff files for annotations I will be ecstatic.
Why doesn't IGV work?
IGV does not plot stranded information above and below the x-axis. I would have to split the bam file then have two separate tracks per strand which does not lend itself to good figures. I tried IGB too which I saw mentioned on some posts but my files are too large and the program freezes up.
You can color the reads by strand.
Doesn't work, unless I'm doing something wrong. Negative strand should be colored red and there's none there. I am confident that my library prep is stranded and there should be signal on both strands.
Oh, I don't know if you can color the pileup, but you can color the reads themselves below.