Hello! I'm trying to analyse some ChIPSeq data from a GEO repository. These files are all in fastq and I easily found a way to download them directly into my Galaxy History. Since they are completely unprocessed data, I should start with mapping them and than convert them. I'm having a lot of problems since the mapping phase gives me an error, saying that my original files contain both Sanger and Illumina info, but the output has been surely obtained by Illumina. Do someone can help me with some suggested tutorial or workflow to move on? Unforunately I've searched on Galaxy community but no suggestions were provided and concerning tutorials, all workflows start from already aligned files.
Thank you for your help!!
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mjdm •
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Since this is a galaxy specific question you may want to post this over at Galaxy Help forum.
Galaxy does have this ChIP-seq tutorial available.
If you want, you can check my workflow (https://github.com/gynecoloji/SnakeMake_ChIPseq). I think I have a relatively complete workflow written in python snakemake.