RT_end_counter

Purpose

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.

Example

You can choose one way from two ways shown below. One is using a docker image in an interactive mode, and another is in a command line-like mode.

1. Analyze on a docker container

docker pull carushi/rt_end_counter
docker run --rm --name reactIDR -it carushi/rt_end_counter

docker cp host/directory/test.bam reactIDR:/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.

• Check the result!

less test_ctss.bed
# RT end count
less test_cov.bed
# Coverage count

2. Use a docker container as a command line tool

docker pull carushi/rt_end_counter
docker run --rm -v /host/directory:/test_data carushi/rt_end_counter count_and_cov.sh -q 10 /test_data/test.bam

@ 2017 carushi