Almost Everything about ChIP-Seq data analysis. Focus on a beginner

[jennaj]

Hello @1113

@1113

I tried to use plotfingerprint and my input and IP samples look like my protein binds to very broad regions. I have heard that for data like that I have to use specific peak caller. Which one?

This help below will aid when getting started with Galaxy. It includes links to the Galaxy GTN Tutorials, which include a ChIP-seq batch of tutorials that cover many tool options, workflows, and examples. If you find a problem with a tutorial, there is a feedback form at the end of each one. If you want to discuss a tutorial for clarification, try the GTN Gitter chat: https://gitter.im/Galaxy-Training-Network/Lobby

Troubleshooting resources for errors or unexpected results

Check to see if there is a known usegalaxy.* server issue. Server Status: https://status.galaxyproject.org/ If the server was down when you first ran your job, try a rerun once back up. A rerun can also eliminate transient server issues too short in duration to trigger a statuspage warning. Next, start by reviewing the troubleshooting FAQ. Common reasons and solutions for tool errors are explained. Most job errors can be resolved by correcting your input data’s format/content. Others indica…

For your other question:

@1113

My first question would be: After using trimmomatic (removing TrueSeq 3 adapters and sliding window), the reads were mapped with BWA-MEM. I removed duplicates and had a pick of the data to see that my sequences mapped only to Chromosome 1… in input and IP samples. That sounds very wrong. May be BAM file can not be all viewed in Galaxy? There is no indications that the file is not fully visible. Or my trimming removed some significant part of good reads?

BAM datasets are very large. A message is shown at the top of the window (after clicking on the “eye” icon) that describes that only part of the data is displayed.

To learn how to generate and interpret statistics on datasets, including BAM datasets, please see this prior Q&A: How to interpret and generate statistics for any dataset, including BAM or SAM or Tabular data

Thanks!