Hello:
I just obtained a set of BAM file that is obtained by Ion Torrent(our collaborator helped with the mapping already).
I used to use galaxy to process illumina reads, MACS in galaxy main instance will convert my SAM/BAM file into wiggle simultaneously while doing peak calling.
Now I found that I cannot do the same for Ion Torrent data(I figure I cannot use MACS to do peak calling because unlike illumina ion torrent reads are not with fixed length).
There is also anther thing very odd: I got a lot of lines like 'Chr NT' in the bam file, what does those mean? I figured that possibly this is what caused the error. Since my computer has only 2Gb ram I cannot use text editor to remove those lines(the BAM file is 3GB in size), is there any similar manipulation I could do by using galaxy?
Thank you in advance for answering the question.
This question should be posted on the Galaxy Support page: https://biostar.usegalaxy.org/
Thank you! I posted it here since I am also looking for alternative ways to do it!