介绍

工具 | deepTools（一） - 图1

BAM 和 bigWig 文件的处理

multiBamSummary

multiBigwigSummary

correctGCBias

bamCoverage

  1. bamCoverage \
  2.   --bam a.bam \
  3.   -o a.SeqDepthNorm.bw \
  4.   --binSize 10 \
  5.   --normalizeUsing RPGC \
  6.   --effectiveGenomeSize 2150570000 \
  7.   --ignoreForNormalization chrX \
  8.   --extendReads
  10. bamCoverage \
  11.   --bam myAlignedReads.bam \
  12.   --outFileName myCoverageFile.bigWig \
  13.   --outFileFormat bigwig \
  14.   --fragmentLength 200 \
  15.   --ignoreDuplicates \
  16.   --scaleFactor 0.5

bamCompare

bigwigCompare

bigwigAverage

computeMatrix

alignmentSieve

参考

  1. https://github.com/deeptools/deepTools
  2. https://deeptools.readthedocs.io/en/latest/
  3. deepTools工具说明