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看看更新頻率拒课，你沒看錯徐勃，前幾天才更新事示。。
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隨便拿一個基因輸入看看（注意這里只支持RAPDB-ID）:Os11g0559200
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首先是這樣的
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選擇右邊的tracks(分析的人都知道僻肖，這一班就意味著各種data),分八個板塊
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比如我們想看組蛋白H3K27me3修飾肖爵，理所當然快捷選擇antibody
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然后我這里選擇看了水稻野生型DJ里面12天葉片的H3K27me3修飾
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可以看到這個基因上幾乎沒有H3K27me3修飾
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特別Nice的是還可以支持導(dǎo)入自己的數(shù)據(jù)，像bw臀脏、gff文件等劝堪。
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其次特別Nice的是給了所有分析腳本
分析命令
$ ./fastq-dump -I SRRxxxxx (for single-end sequencing)
$ ./fastq-dump -I --split-files SRRxxxxx (for pair-end sequencing)
- 使用軟件版本以及質(zhì)量過濾說明
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).
比對到基因組
$ 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.
將sam文件轉(zhuǎn)換成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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腳本內(nèi)容
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Before running the script, several tools need to be installed and added to your executable path.
