Question: Tool/scripts for quantifying proportion of aligned RNA-seq reads on the basis of their types ?
gravatar for Siddharth
2.6 years ago by
Siddharth0 wrote:

I'm working with RNA-seq data and I'm already done with alignment(i.e. I have the BAM files). My question is:

Is there a tool or script which can quantify the aligned reads on the basis of their types, i.e. mRNA, lncRNA, miRNA etc just from the alignment files (BAM ) and annotation files (GTF/BED). I need the data in form of number of aligned reads belonging to each RNA type. The reason I need that data is because I want to plot the population of each type for each alignment file I have.

Thank you!

python rna-seq alignment R • 686 views
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