I'm a real beginner in the field of ChIP-seq analysis and bioinformatics in general (so please be patient) and wondered if you could help. I am trying to analyse my TFBS ChIP-seq data with Galaxy using the guidelines in the following paper:-
Bailey et al. "Practical guidelines for the comprehensive analysis of ChIP-seq Data", PLOS Computational Biology 2013
I have so far managed to do FastQC, trimming and grooming of my FASTQ data before aligning with Bowtie2. I now want to look at the quality metrics of my sequence reads specifically my library complexity. I can see from my BAM files that I have around 68% of uniquely mapped reads so maybe a little below ideal but I would like to proceed and look at the library complexity i.e., the number of genomic locations that my uniquely aligned reads map to.
Where/how can I find this information and generate scores/ratios for this? Is there a tool in Galaxy that will do this for me? I tried the "Estimate Library Complexity" function but I didn't seem to get anything useful back from it. There seems to be a "Collect RNA-seq Metrics" function that also didn't give me what I'm looking for.
Is there something I'm missing in my BAM file or a tool that is not available in Galaxy to do this for me? I have absolutely no experience with R and would take me a long time to get up and running with it so any non-R related solutions would be greatly appreciated!