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titleclick here to see the code for bedtools coverage
Code Block
languagebash
titlesolution code
module load bedtools #again, if not already loaded
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

And here is what my output looks like:

Code Block
languagebash
more sacCer3coverage.bed
chrI      1    230218    7972     128701    230217    0.5590421
chrII     1    813184    35818    539222    813183    0.6631004
chrIII    1    316620    13701    199553    316619    0.6302623
chrIV     1    1531933    70633    1026387    1531932    0.6699951
chrIX     1    439888    15953    276571    439887    0.6287319
chrM      1    85779     3264     58599     85778     0.6831472
chrV      1    576874    26918    381078    576873    0.6605926
chrVI     1    270161    10662    167222    270160    0.6189740
chrVII    1    1090940    49762    722821    1090939    0.6625677
chrVIII    1    562643    23424    356421    562642    0.6334774
chrX      1    745751    30743    472357    745750    0.6333986
chrXI     1    666816    27950    446567    666815    0.6697015
chrXII    1    1078177    48155    658373    1078176    0.6106359
chrXIII    1    924431    40054    618798    924430    0.6693833
chrXIV    1    784333    32565    513382    784332    0.6545468
chrXV     1    1091291    47871    710376    1091290    0.6509507
chrXVI    1    948066    43531    612122    948065    0.6456540

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