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Calculate Coverage :: Bedtools
agaszmurlo edited this page Aug 30, 2018
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3 revisions
How to calculate coverage (strand specific) using bedtools
- Pull Bedtools Docker image
docker pull biocontainers/bedtools- In your data folder create calc_cov.sh. Clone from GitHub and copy to your data folder.
git clone git@gist.github.com:3d9585ae1247ae54d41e7377f8ff49a6.git
cd 3d9585ae1247ae54d41e7377f8ff49a6
cp calc_cov.sh /data/samples/sequila-rna/data/dane
cd /data/samples/sequila-rna/data/dane
chmod 777 calc_cov.sh
ls
calc_cov.sh fastq hisat star star1 star_bardzo_ograniczone star_mniej_ograniczone star_najbardziej_ograniczone - Run calc_cov.sh
./calc_cov.sh
Calculating coverage for star_najbardziej_ograniczone/sample_01Aligned.sortedByCoord.out.bam.
Output: coverage/star_najbardziej_ograniczone/sample_01Aligned.sortedByCoord.out.bed. Time taken: 16 s.
Calculating coverage for star_najbardziej_ograniczone/sample_02Aligned.sortedByCoord.out.bam.
Output: coverage/star_najbardziej_ograniczone/sample_02Aligned.sortedByCoord.out.bed. Time taken: 12 s.
Calculating coverage for star_najbardziej_ograniczone/sample_03Aligned.sortedByCoord.out.bam.
Output: coverage/star_najbardziej_ograniczone/sample_03Aligned.sortedByCoord.out.bed. Time taken: 13 s.
Calculating coverage for star_najbardziej_ograniczone/sample_04Aligned.sortedByCoord.out.bam.
Output: coverage/star_najbardziej_ograniczone/sample_04Aligned.sortedByCoord.out.bed. Time taken: 14 s.
Calculating coverage for star_najbardziej_ograniczone/sample_05Aligned.sortedByCoord.out.bam.
Output: coverage/star_najbardziej_ograniczone/sample_05Aligned.sortedByCoord.out.bed. Time taken: 13 s.
Calculating coverage for star_najbardziej_ograniczone/sample_06Aligned.sortedByCoord.out.bam.
Output: coverage/star_najbardziej_ograniczone/sample_06Aligned.sortedByCoord.out.bed. Time taken: 11 s.
Calculating coverage for star_najbardziej_ograniczone/sample_07Aligned.sortedByCoord.out.bam.
Output: coverage/star_najbardziej_ograniczone/sample_07Aligned.sortedByCoord.out.bed. Time taken: 12 s.
...- Results are in coverage directory
aszmurlo@cdh00:/data/samples/sequila-rna/data/dane> head coverage/star/sample_01Aligned.sortedByCoord.out.bed
22 0 10678908 0 +
22 0 10678908 0 -
22 10678908 10678968 5 +
22 10678908 10678968 5 -
22 10678968 10872376 0 +
22 10678968 10872376 0 -
22 10872376 10872436 20 +
22 10872376 10872436 20 -
22 10872436 10959132 0 +
22 10872436 10959132 0 -