Add rule to generate normalized coverage tracks

In order to compare coverages in genome browsers, it is desirable to scale them across samples. Add a rule that converts a BAM file to a coverage (e.g., wiggle or bedgraph format) track that is scaled by a constant factor.

@burri0000 Do you think that this issue will be fixed by https://git.scicore.unibas.ch/zavolan_group/pipelines/rnaseqpipeline/blob/alfa_qc/snakemake/paired_end.snakefile.smk#L342-402 or do we need another normalization or/and file?

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@gypas could you please give some more context here? And while you're add it, put a proper concise title? :)

The rule you mention computes the normalised coverage per .bam. Adina and I described it here https://git.scicore.unibas.ch/zavolan_group/pipelines/rnaseqpipeline/issues/18#note_15138.

So this rule generates Read-per-million normalised coverage tracks (.bedgraph or wiggle) for stranded (i.e. separated strands) data. A unstranded version is possible as well. However, I think at least, it can only take one .bam at a time and I generally one .bam corresponds to one library.

@kanitz When you open some mapped reads with IGV and you want to compare two samples (by eye) you can't do that, as the files are not normalized. What you need to do is to scale the coverage by a constant factor. A useful way of normalizing reads is the Reads Per Million (RPM).

changed title from Add a script that takes as input a list of BAM files and exports them to a format (BAM/bigwig/...) where the data are library size normalized for IGV view to Normalised coverage track for view in IGV

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changed title from Normalised coverage track for view in IGV to Normalised coverage track for view in genome browsers

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changed title from Normalised coverage track for view in genome browsers to Normalize coverage track for view in genome browsers

changed title from Normalize coverage track for view in genome browsers to Normalized coverage tracks for use in genome browsers

changed title from Normalized coverage tracks for use in genome browsers to Add rule to normalize coverage tracks

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changed title from Add rule to normalize coverage tracks to Add rule to generate normalized coverage tracks

assigned to @burri0000

Add rules to generate .bedgraph from .bam with STAR on new branch.

mentioned in commit 5667e68d