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Exercise 1: convert bam to fastq and look at the quality scores
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| title | Solutionclick here to see the code |
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| language | bash |
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| title | solution code |
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| module load bedtools
bedtools bamtofastq -i yeast_pairedend_sort.mapped.q1.bam -fq yeast_pairedend_sort.mapped.q1.fastq
more yeast_pairedend_sort.mapped.q1.fastq |
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Exercise 2: Convert the filtered yeast paired end bam to bed using bamtobed, look at your file in more, and find the number of lines in the file
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| title | Solutionclick to see the code |
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| language | bash |
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| title | solution code |
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| module load bedtools
bedtools bamtobed -i yeast_pairedend_sort.mapped.q1.bam > yeast_pairedend_sort.mapped.q1.bed
more yeast_pairedend_sort.mapped.q1.bed #to examine the bed file visually
wc -l yeast_pairedend_sort.mapped.q1.bed #to get the number of lines in a file |
use ctrl+c to quit more |
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Exercise 3: Find the coverage of your bed file over the sacCer3 genome
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| title | Solutionclick here to see the code for bedtools coverage |
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| language | bash |
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| title | solution code |
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| module load bedtools
bedtools coverage -a yeast_pairedend_sort.mapped.q1.bed -b sacCer3.chrom.sizes.bed > sacCer3coverage.bed
more sacCer3coverage.bed #this file should have 17 lines, one for each chromosome |
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Hint: make sure to remove whitespace between lists for the -c and -o options!
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| title | Solutionclick here to see the bedtools merge code |
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| language | bash |
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| title | solution code |
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| bedtools merge -c 4,5,6 -o distinct,sum,distinct -i yeast_pairedend_sort.mapped.q1.bed > yeast_pairedend_sort.mapped.q1.merge.bed
more yeast_pairedend_sort.mapped.q1.merge.bed
wc -l yeast_pairedend_sort.mapped.q1.merge.bed |
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| title | bam filtering and bed conversion of human bam files |
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| module load bedtools
#filtering the bam files
#converting the filtered bam files into bed files
bedtools bamtobed -i yeast_pairedend_sort.mapped.q1.bam > yeast_pairedend_sort.mapped.q1.bed |
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Exercise 5: Intersect two experiments using intersect
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