Projection to the reference genome for reads

[tyomach]

As I understand MEA performs projection to the reference genome for coverage data (bedgraph or bw). Is it also possible to do the same for read level files (bam)? What I would like to get is the number of reads mapped to allele1 or allele2 for each polymorphism in the reference genome coordinates.
Thanks foryour advice.

[julienrichardalbert]

You understanding is correct. Unfortunately there is no read-level projection compatibility to date.. We tried developing such a read-projection script for a few months but could not work out the various CIGAR string problems that arise.
Read count estimates can be inferred from coverage data if read lengths are standard and known, but it is just an approximation.
During our attempts to develop a bam-projection script, we made a decent bed projection script that I am happy to share. Converting a bam to bed, where each entry are the coordinates of the aligned read, then projecting the bed onto the reference and counting entries, would be another workaround.

[tyomach]

This will be great. We can try to work with the bed projection.
Thanks!

[julienrichardalbert]

First, we use this to re-order chromosomes of the refmap file
$SortRefmap.sh ALT.refmap ALT.sort.refmap
Then, with the sorted refmap file, project bed script
$awk -f ProjectBed.awk ALT.sort.refmap file.bed > file.projected.bed
Scripts attached: projectBed.zip

Good luck!