ChIP seq Motif analysis

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Question: ChIP seq Motif analysis

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7 months ago by

sonam.rani • 10

sonam.rani • 10 wrote:

Hi,

How to do motif analysis after peak calling? I used MACS2 for peak calling, used fastq to fasta converter, the Fasta file was groomed using FASTQ groomer to proceed with motif analysis with MEME... It shows error while grooming .. How can I do motif analysis after peak calling with MACS2?

motif meme macs2 chip-seq • 509 views

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modified 7 months ago by Jennifer Hillman Jackson ♦ 25k • written 7 months ago by sonam.rani • 10

1

7 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Fasta datasets and even most fastq datasets do not need to be run through the Fastq Groomer. It is only needed when the fastq data has quality scores from an older NGS protocol that need to be rescaled.

An overview of NGS data preparation and ChIP-seq analysis can be found in the Galaxy tutorials: https://galaxyproject.org/learn/

NGS logistics - this is an introduction to Galaxy's functionality for the analysis of Next Generation Sequencing data. https://galaxyproject.org/tutorials/ngs
ChIP-seq: A simple ChIP-seq experiment with two replicates - an example analysis for finding transcription factor binding sites. https://galaxyproject.org/tutorials/chip

Help with technical data formatting and manipulations are covered in the Galaxy Support FAQs: https://galaxyproject.org/support/

See the help regarding fastq data and custom genomes (CG format rules apply for all fasta datasets used within Galaxy): https://galaxyproject.org/support/#getting-inputs-right
Common reasons for job failures are also covered, please see: https://galaxyproject.org/support/#unexpected-results

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson ♦ 25k

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Thank you Jennifer...!!

ADD REPLY • link written 7 months ago by sonam.rani • 10

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