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telatin / bamtocov

🏔 coverage extraction from BAM/CRAM files, supporting targets 📊  
https://telatin.github.io/bamtocov/
MIT License
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add an argument for bamtocov to allow the extension of reads to fragment size from single-end sequencing data #6

Open kerenzhou062 opened 2 years ago

kerenzhou062 commented 2 years ago

Is your feature request related to a problem? Please describe. In most of the IP-based methods, we need to extend reads to the fragment size to get the correct coverage for real IP regions if we sequence in a single-end mode.

Describe the solution you'd like Add similar arguments with "--extendReads" from bamCoverage of deeptools would be a very good option.

telatin commented 2 years ago

To clarify, you would need a --extendReads INT that will artificially count the read coverage from the read starting base to INT base downstream?

kerenzhou062 commented 2 years ago

To clarify, you would need a --extendReads INT that will artificially count the read coverage from the read starting base to INT base downstream?

This option will artificially count the read coverage from read starting base to INT base downstream of ending base. That means extending the read length by INT bp from 5' to 3' direction. Thanks!

telatin commented 2 years ago

As an experimental feature, I added --extendRead INT in bamtocov today, that will artificially set the end of an alignment at (alignment start + INT) nucleotides (or the end of the chromosome, whichever smaller.

kerenzhou062 commented 2 years ago

As an experimental feature, I added --extendRead INT in bamtocov today, that will artificially set the end of an alignment at (alignment start + INT) nucleotides (or the end of the chromosome, whichever smaller.

Thank you so much for your updates. This feature will be very helpful!