Question: ChIP-seq paired-end analysis
0
chelouah_sonia • 0 wrote:
Could you help me to understand how to analyze the data CHIP- seq paired-end on galaxy ?
Thank you.
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0
Dannon Baker ♦ 3.7k wrote:
Do you have any particular questions about the analysis, or do you just need some help getting started?
For the latter, here's an example that might help you out: https://usegalaxy.org/u/james/p/exercise-chip-seq
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chelouah_sonia • 0 wrote:
Hi Dannon,
I have a question about running MACS tool for my chip-seq data to call the peaks in Galaxy.
My data is pair-end sequenced. I have already upload the BAM mapping file I want to run MACS tool under the “Paired End Sequencing” but it asks for the ELANDMULTI format and for tow ChIP-seq Tag files.
How can I get the ELANDMULTI format dataset ? Do I only map each file Fastq R1 and R2 before starting MACS tool ?
Thank you
Sonia
I don't think there's actually a tool on usegalaxy.org for creating elandmulti files. The last advice I heard for this was to use the Cistrome Galaxy to create this file (http://cistrome.org/ap/root), but other than that I'm not familiar enough with this to offer much advice -- perhaps someone else can chime in here.
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Hi all,
I have a question about running MACS tool for my chip-seq data to call the peaks in Galaxy.
My data is pair-end sequenced. I have already upload the BAM mapping file I want to run MACS tool under the “Paired End Sequencing” but it asks for the ELANDMULTI format and for tow ChIP-seq Tag files.
How can I get the ELANDMULTI format dataset ? Do I only map each file Fastq R1 and R2 before starting MACS tool ?
Thank you