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SX知识学习——CHIPseq(转+总结)

时间:2018-03-25 12:00:42      阅读:230      评论:0      收藏:0      [点我收藏+]

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http://www.htslib.org/workflow/#mapping_to_variant

分析流程:
step0—安装相关软件

step1—下载参考基因组数据和分析数据以及原始测序数据sra格式转换为fastq格式

sratoolkit :https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

sratoolkit documentation:https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc

如:

  ls *.sra |while read id; do ~/biosoft/sratoolkit/sratoolkit.2.6.3-centos_linux64/bin/fastq-dump $id;done

  rm *sra

step2—质控fastqc、去低值FASTX-Toolkit再质控

(1)

  ls *.fastq | while read id ; do ~/biosoft/fastqc/FastQC/fastqc $id;done

Then we need to filter the bad quality reads according to the QC results.

##write a script by cat >filter.sh

(2)

  ls *fastq |while read id

 

  do

  echo $id

## you need to adjust the parameter by yourself according to the QC results.

  ~/biosoft/fastx_toolkit_0.0.13/bin/fastq_quality_filter -v -q 20 -p 80 -Q33 -i $id -o tmp ;

  ~/biosoft/fastx_toolkit_0.0.13/bin/fastx_trimmer -v -f 1 -l 27 -i tmp -Q33 -z -o ${id%%.*}_clean.fq.gz ;

  done

  rm tmp

(3)

  ls *_clean.fq.gz | while read id ; do ~/biosoft/fastqc/FastQC/fastqc $id;done

step3—alignment(bowtie2)

(1)build index

  ~/biosoft/bowtie/bowtie2-2.2.9/bowtie2-build ~/biosoft/bowtie/hg19_index /hg19.fa ~/biosoft/bowtie/hg19_index/hg19

(2)alignment

  ls *.fastq | while read id ;

  do

  echo $id

  ~/biosoft/bowtie/bowtie2-2.2.9/bowtie2 -p 20 -x ~/biosoft/bowtie/hg19_index/hg19 -U $id -S ${id%%.*}.sam 2>${id%%.*}.align.log;

(3)## *.sam to *.bam

  samtools view -bhS -q 30 ${id%%.*}.sam > ${id%%.*}.highQuality.bam

  (http://www.htslib.org/doc/samtools.html)

  ## -F 1548 https://broadinstitute.github.io/picard/explain-flags.html

  samtools sort ${id%%.*}.highQuality.bam ${id%%.*}.highQuality.sorted

  samtools index ${id%%.*}.highQuality.sorted.bam

 

(4)unique mapping reads

  grep -v "XS:i:" ${id%%.*}.sam |samtools view -bhS - >${id%%.*}.unique.bam

  amtools sort ${id%%.*}.unique.bam ${id%%.*}.unique.sorted

  samtools index ${id%%.*}.unique.sorted.bam

  done

step4—peaks-calling-by-macs2

 

      

 

SX知识学习——CHIPseq(转+总结)

标签:-o   color   sort   uil   yourself   转换   unique   grep   AC   

原文地址:https://www.cnblogs.com/fangfang66/p/8643042.html

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