Question: How to convert ion torrent Reads into Wiggle by galaxy?
0
gravatar for muhe1985
4.6 years ago by
muhe198510
United States
muhe198510 wrote:

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.

 

chip-seq • 1.5k views
ADD COMMENTlink written 4.6 years ago by muhe198510

This question should be posted on the Galaxy Support page: https://biostar.usegalaxy.org/

ADD REPLYlink written 4.6 years ago by Istvan Albert ♦♦ 80k

Thank you! I posted it here since I am also looking for alternative ways to do it!

ADD REPLYlink written 4.6 years ago by muhe198510
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