Collapse mapped reads in sorted bam file based on the start and end position coordinates

Question

[xiaoleiusc]

Dear Biostars Users,

Is there a way to collapse mapped reads in sorted bam files based on the start and end position coordinates regardless of sequences? I would like to collapse the number of reads with the same start and end position as "1" although these reads have different sequences. I attach an image here [ https://ibb.co/J7Fj00T] to illustrate my points if not clear in words.

Thanks ahead.

Xiao

[GenoMax]

Use: How to add images to a Biostars post

[Collin Rukundo]

Thanks man. This is right on

[xiaoleiusc]

Thanks, I followed your suggestions and re-uploaded my image. Feel free to let me know if there is any problem.

[benformatics]

You could do this in R with GenomicRanges/Alignments relatively easily

Answer 1

[GenoMax]

Sounds like you need to clumpify your reads BEFORE you align them (to remove sequence duplicates): A: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files

[xiaoleiusc]

Thanks Genomax, could Clumpify remove sequence duplicates with different sequences? I removed my sequence duplicates with FastX-toolkits (FASTQ/A Collapser) before mapping. Now I consider more stringent criteria of duplicates: reads mapped to the references that have the same start and end position in the alignment. Note that the sequences of these reads can be different.

[GenoMax]

clumpify will do that but not using the aligned BAM files. To get the result you need, you will need to first collapse the reads (clumpify allows errors, hdist=Number parameter, so reads containing one or more SNP's can be treated as having identical sequence). Then follow that by alignment.