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| Code Block |
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| language | bash |
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| title | copy some files over to intersect |
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cdscd $SCRATCH/core_ngs/
mkdir intersect
cd intersect
cp /scratch/02423/nsabell/core_ngs/alignment/bam/alignment/
samtools view -b human_rnaseq_mem.sam > human_rnaseq_bwamem.bam
samtools view -b human_mirnaseq.sam > human_mirnaseq.bam
cp /scratch/02423/nsabell/core_ngs/alignment/bam/human_rnaseq_mem.bam ../intersect
cp human_mirnaseq_hg19.bam ../intersect
cd ../intersect
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| Expand |
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| title | click here to see my output on copying files |
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| Code Block |
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| -rwxrwxr-x-rw-rw-r-- 1 awh394 G-801021 19M16M May 2722 1418:1736 human_mirnaseq_hg19.bam
-rwxrwxr-x-rw-rw-r-- 1 awh394 G-801021 69.6M1M May 2722 1418:1736 human_rnaseq_bwamem.bam |
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Before we can intersect these files, we need to perform the pipeline we used in samtools to index, sort and filter the files, and bedtools to convert from BAM over to bed, then collapse down the files using merge. Below is a little workflow to help you through it on the files you just copied above.
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