Docker image which contains samtools, bedtools2, and RT end counter.
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 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 out. bash count_and_cov.sh -l 100 /docker/directory/test.bam # Reads whose length is less than 100 are remanied. bash 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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