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Last pushed: a month ago
Short Description
Docker image which contains samtools, bedtools2, and RT end counter.
Full Description

RT_end_counter

Purpose

This repository is to construct Docker image which contains samtools, bedtools2, and RT end counter for high-throughput structure analyses such as icSHAPE, PARS, and DMS-seq.

Example

docker pull carushi/rt_end_counter
docker run -it carushi/rt_end_counter /bin/bash
docker cp host/directory/test.bam container_id(e.g.aabbcc112233):/docker/directory/
bash count_and_cov.sh /docker/directory/test.bam

bash count_and_cov.sh -q 10 /docker/directory/test.bam
# Reads whose quality is less than 10 are filtered.

count_and_cov.sh -k /docker/directory/test.bam
# Keeps temporary files for debug.
less test_ctss.bed
# RT end count
less test_cov.bed
# Coverage count

@ 2017 carushi

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carushi
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