Information regarding input file types

[Nirmalya Saha]

Hi,

I am new to ChIP-seq analysis. I have a question regarding input files to run MAnorm. Correct me if I am wrong in understanding the input file types.

Among the 4 files XXX_peak.bed file is generated by MACS (the peak caller). Is that correct? What about this file sample1_readfile.bed? I donot undersatnd the meaning of this file. neither I know how is this file gonna be generated?

Thanks in advance

Your help will be greatly appreciated

[shaozh...@gmail.com]

Hi Nirmalya,

Glad to hear you are interested to use MAnorm. Sorry for seeing this email so late. Now it's not easy to access gmail in China. You can contact me via shao...@picb.ac.cn if you have further questions. 

Yes, XXX_peak.bed file is the file containing peak information, and MAnorm can directly take the output from MACS. And sample1_readfile.bed is ChIP-seq raw data of bed format. Usually you can directly get it from the guy who provides you the ChIP-seq data.

Zhen

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shaozh...@gmail.com

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[Mayuri Rege]

Hi Nirmalya and Zhen,

I have analyzed my own ChIP-seq data (from FASTQ to Peak calling) and now I want to use MAnorm to do normalization on my dataset.

I have the same question as this: I can't figure out what the "sample1_readfile.bed" is? 

Is it the alignment file obtained after mapping to the genome (SAM/BAM)?

The example files in the MAnorm download don't have more details either: 

sample1_peaks.bed (has 1000 lines) and is of the following format:

chr start end

sample1_reads.bed (has 10000 lines) and is of the following format:

chr start end strand

How do we generate the sample1_reads.bed file? 

Thanks!

Mayuri

Graduate student
Suite 203, Two Biotech
University of Massachusetts Medical School
373 Plantation St.
Worcester, MA 01605

[Mayuri Rege]

Thank you for your replies, Nirmalya and Andy. I am just posting the answer for the sake of completion.

"Yes, the "sample1_readfile.bed" is the alignment file obtained after mapping.  You can use a BEDTools command: bamtobed.  You should check that the resulting BED file has the correct positions for a few example reads."

[shaozh...@gmail.com]

Hi Mayuri,

Thanks for your interests in using MAnorm and sorry for answering late. I'm in China now and very hard to access google group. 

Besides, we are re-writting MAnorm and some associated applications using Python and hopefully will publish them soon.

If you are interested in our works, you can heep an eye on our website: 

http://bioinfo.sibs.ac.cn/shaolab/index.php 

Best,

Zhen 

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shaozh...@gmail.com

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