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



This repository is associated with the docker image, which contains samtools, bedtools2, and RT end counter for high-throughput structure analyses such as icSHAPE, PARS, and DMS-seq.


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 /docker/directory/test.bam

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

bash -l 100 /docker/directory/test.bam
# Reads whose length is less than 100 are remanied.

bash -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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