Hi guys, I'm analysing acChipSeq data. I performed all the steps of a canonical best practice pipeline. The last step was the coverageBed. Now, since I would like to perform a differential analysis for example using edgeR I need to have a matrix in which rows are genes and columns are samples. The output of the coverageBed is a file that looks like this:
chr1 9884 10032 0 0 148 0.0000000
chr1 191374 191638 0 0 264 0.0000000
chr1 270604 271602 0 0 998 0.0000000
chr1 272675 272855 0 0 180 0.0000000
It is a .bed file. Since I cannot use FeatureCount with bed files I converted to .bam but they are always corrupted. Any suggestion to have a classical table with genes as rows and samples as columns as FeatureCount does with canonical RNA seq data analysis?
Thank you in advance
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Bnf83
1 answer
The reason the bam file is not working is because the bed file doesn't contain enough information to re-create reads. Perhaps there is a tool that attempts to reconstruct reads based on coverage beds, but that sounds...not good. You need a true bam/sam for featureCounts.
I am unfamiliar with the acChipSeq protocol, but standard ChipSeq uses a mapping tool to generate a bam/sam at some point upstream of the bed file generation. You want that intermediate file.
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