I am new to Galaxy. I need to analyse my Chip-Seq data.I found very useful training resources of Galaxy:
and also about using Galaxy for Chip-Seq data analysis from Abcam:
However, it is not enough for a complete beginner. I am missing a discussion where I can ask about specific cases and tools application. For example, why in Chip-seq Galaxy tutorial we use BWA-MEM not Bowtie2 for mapping? Why we do not trim adapters with trimmomatic? What to do with 4 files produced by trimmomatic (when you trim adapters ir produces 2 files with paired reads and 2 fails for unpaired reads) etc. There is a whole section on ChIP-seq in Galaxy. What is there? and of course: What my results mean
Some answers could be found on other forums. It would be very useful to have a good discussion in one place. For example here where we can share our experiences using Galaxy for Chip-seq data
I plan to post my questions here.
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?
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?
Thank you all!