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griffithlab / regtools

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
https://regtools.readthedocs.org
MIT License
121 stars 26 forks source link

Feature request #183

Open Mohamed-HAMICI opened 8 months ago

Mohamed-HAMICI commented 8 months ago

Hello,

First of all, thank you for this tool that is so easy to use. I am currently using it for the extraction and annotation of BAM files and it works very well. I thought it may be a good idea if we could have the option to exclude the duplicate reads in the junction count.

Thanks for reading me.

yfarjoun commented 4 months ago

I would like to support this request and expand it to allow a samtools-style -f and -F arguments for required flags and filtered flags