Question: How to convert ion torrent Reads into Wiggle by galaxy?
1
gravatar for yewenduo
4.2 years ago by
yewenduo60
United States
yewenduo60 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 • 1.4k views
ADD COMMENTlink modified 4.1 years ago by Jennifer Hillman Jackson25k • written 4.2 years ago by yewenduo60
1
gravatar for Jennifer Hillman Jackson
4.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The basic steps to convert Bam to wiggle (wig) are: 

  1. BEDTools: Create a BedGraph of genome coverage
  2. Convert Formats: Wig/BedGraph-to-bigWig converter

Note that this is NOT the same thing as calling peaks. Those algorithms do more that count positional read depth from a mapping jobs. 

But I think you will need to solve the reference genome issue first, if that is the immediate issue (not exactly clear, but you can check).
http://wiki.galaxyproject.org/Support#Reference_genomes

"Chr NT" looks like a chromosome identifier to me. The reference genome used for mapping and that used by downstream tools must be identical. Check for a conflict with what you are using now, then consider using a Custom reference genome (obtain the .fasta from your colleague that did the mapping).
https://wiki.galaxyproject.org/Support#Custom_reference_genome

I would normally suggest adding in the genome natively to your instance, instead of using a Custom genome, but any of these operations will have problems running with so little memory. A good rule to follow is that if the tool will run line-command on a system, it will almost certainly run within Galaxy (same core resources are needed for the tool's operation).

Because of that, consider a larger server for processing:

  1. Main, http://usegalaxy.org
  2. Cloud, http://usegalaxy.org/cloud
  3. All options, http://wiki.galaxyproject.org/BigPicture/Choices

Best, Jen, Galaxy team

ADD COMMENTlink written 4.1 years ago by Jennifer Hillman Jackson25k

thank you very much!!!!

ADD REPLYlink written 4.1 years ago by yewenduo60

Hi, Jen:

If I were to ignore those Chr MT/NT, could you give me a suggestion how to do that in galaxy? if it was a smaller file I could just delete those lines by notepad++ by regular expression, but this file exceeded my computer capacity since it is too big. Can I do any regular expression maneuver in galaxy?

Thank you again!

ADD REPLYlink written 4.1 years ago by yewenduo60

Hello,

The Select tool permits regular expression use. But the Filter tool may be a more direct method if just working with a single column and known filter criteria.

With either tool, you'll need to work with tabular data. BAM is compressed, so a BAM-to-SAM run with Samtools would be needed. Not sure how much disk you have, or if this will cause a problem with memory. Worth a try locally, then use a larger server if problems. This particular tool does not require a reference genome, so that is good. Going back the other way will - and if the genomes are not an exact match, expect to encounter issues.

ADD REPLYlink written 4.1 years ago by Jennifer Hillman Jackson25k

thank you! I am trying according your instructions in galaxy main.

ADD REPLYlink written 4.1 years ago by yewenduo60
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour