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看看更新频率，你没看错，前几天才更新。。
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随便拿一个基因输入看看（注意这里只支持RAPDB-ID）:Os11g0559200
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首先是这样的
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选择右边的tracks(分析的人都知道，这一班就意味着各种data),分八个板块
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比如我们想看组蛋白H3K27me3修饰，理所当然快捷选择antibody
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然后我这里选择看了水稻野生型DJ里面12天叶片的H3K27me3修饰
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可以看到这个基因上几乎没有H3K27me3修饰
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特别Nice的是还可以支持导入自己的数据，像bw、gff文件等。
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其次特别Nice的是给了所有分析脚本
分析命令
$ ./fastq-dump -I SRRxxxxx (for single-end sequencing)
$ ./fastq-dump -I --split-files SRRxxxxx (for pair-end sequencing)
- 使用软件版本以及质量过滤说明
Reads qualities were analyzed with FastQC (v0.10.1) and the low quality bases (less than 30) were ignored in the following mapping step.
All the raw reads were mapped to corresponding genomes with Bowtie2 (v2.3.4) and compressed to binary files using samtools (v1.7).
比对到基因组
$ bowtie2 -5 xx -3 xx -x /directory/tair10 -U file.fastq -S file.sam
- Here, xx representsthe the position of the base will be trimmed from the reads before mapping. -5 and -3 indicates the direction of trimming (5’ end and 3’end, respectively); -x and tair10 indicate the mapping index. The index has to be built before mapping. Please see detail in bowtie2 manual.
将sam文件转换成bam文件
$ samtools view -bS file.sam > file.bam
$ samtools sort -T file -o file_sort.bam file.bam
$ samtools index file_sort.bam
- Finally, the mapped reads were converted to bigwig format for visualization by using bamcoverage (deeptools2) with the following settings: binsize 10, normalizing with 1x genome content (RPGC, Arabidopsis thaliana, 135,000,000; Glycine max, 978,000,000; Oryza sativa, 375,000,000; Zea mays, 2,135,000,000), ignorDuplicates, samFlagExclude 1796 and 1924 for single and pair-end sequencing, respectively. The following command will convert single-end Arabidopsis thaliana sorted bam file to bigwig file.
$ bamCoverage -b flie_sort.bam -o file_sort.bw -bs 10 --effectiveGenomeSize 135000000 --normalizeUsing RPGC --ignoreDuplicates -e 100 --samFlagExclude 1796
2.1.3 Generating peak plateau, FRiP, and median enrichment
- The following shell and three R scripts are used for generating figures of peak plateau, FRiP, and median enrichment from mapped binary file (bam file). A list of file name needs to be provided before running the script. All the files including scripts, bam files, and listshould be in the same directory.
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脚本内容
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Before running the script, several tools need to be installed and added to your executable path.
