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trev-f / SRAlign

a flexible pipeline for short read alignment to a reference
MIT License
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Add Encode library complexity metrics #15

Open trev-f opened 2 years ago

trev-f commented 2 years ago

Add library complexity metrics from Encode: Non-redundant fraction (NRF) and PCR bottleneck coefficients 1 and 2 (PCB1 and PCB2). Example code can be seen in Yiewei Niu's ATAC-seq data analysis: from FASTQ to peaks .

trev-f commented 2 years ago

Checkout the code used in ENCODE ATAC-seq pipeline.

Function to run shell commands in a python script.

Functions to compute PCR bottlenecking coefficients.

trev-f commented 2 years ago

No need to use a python script to run shell commands since this can just be done in Nextflow.