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數(shù)據(jù)分析之peakfinder
ChIPSeq Peak Finder
程序下載地址
總體而言，因為程序都是一堆 python 腳本，寫的很分散，所以感覺用
起來不是很好用，所以現(xiàn)在開始測試這個程序。
Peak finder 解壓，數(shù)了數(shù)，一共有17 *.py 文件，也沒作什么合并
所以幾天都沒有跑起來
I.程序文檔的基本解讀
1.
You will want to first convert Solexa output for the chip
and the control sample into bed files using one of the
following scripts:
maketrackfromeland.py
maketrackfromrealign.py
覆蓋 Solexa 輸出到 chip, 使用這兩個腳本控制 示例 到 基準文件
2.
The following scripts are used to read the output from the
0.3 version of ELAND run with the --multi option:
maketrackfromeland2.py
maketrackmulti.py
下面的腳本用于讀 ELAND 0.3版本的輸出， 使用 --multi 選項
3.
You can also create a bed-formatted WIG file, for display
The following scripts are used to read the output from the
0.3 version of ELAND run with the --multi option:
maketrackfromeland2.py
maketrackmulti.py
你也能創(chuàng)建一個 基準 WIG 文件，以上的腳本用于讀 ELAND 0.3 版本
的輸出， 使用 --multi 選項
4.
You will want to first convert Solexa output for the chip
and the control sample into bed files using one of the
following scripts:
maketrackfromeland.py
maketrackfromrealign.py
Chip 到 Solexa 輸出的轉(zhuǎn)換，控制 示例 到 基準文件.
5.
on the UCSC browser:
makewiggle.py
USCE 瀏覽器， 這個腳本什么作用?
6.
The main script actually implements the peak finder:
findall.py
peak finder 實際執(zhí)行的主腳本
7.
You will want to first convert Solexa output for the chip
and the control sample into bed files using one of the
following scripts:
maketrackfromeland.py
maketrackfromrealign.py
on the UCSC browser:
findallnocontrol.py
文件轉(zhuǎn)換 和 示例 矯正 到 基準，作者推薦使用第一個腳本
8.
NEW FEATURE of findall.py : as of version 2.0, you can
/ should use the -normalize option to calculate
everything as Reads Per Million (RPM). While we have
kept the original behavior as default, we will switch
-normalize to be the default in the next release.
findall.py 腳本的新特征: version 2.0 可以使用-normalize
選項計算每個RPM(Reads Per Million). 我們默認保持原樣，下
一個版本將會打開 -normalize
The philosophy of this peak finder is to define regions,
and then search for the motif. However, the findall
script can report the actual peaks in the region with
the -listpeak option.
peak finder 的哲學是定義區(qū)域, 搜索模體。盡管這樣， findall
腳本報告實際的峰的區(qū)域，選項， -listpeak
9.
The rest of the analysis depends heavily on Cistematic
to run. The following scripts find associated genes and
anlyze their GO ontology enrichment, if any:
getallgenes.py
analyzego.py
基于 Cistematic 的其余分析，關聯(lián) 基因 和 GO 富集
10.
The following scripts, also requiring Cistematic,
the sequence in the enriched regions, find motifs using
Meme and map motif sites in regions around the peaks:
getfasta.py
findMotifs.py
getallsites.py
其余腳本， 也要求 Cistematic, 恢復富集區(qū)域的序列，使用
MEME 尋找模體，比對peak附近的模體區(qū)域
11.
The output of findMotifs.py and input of getallsites.py
are motifs in the Cistematic .mot format. A modified
version of getallsites.py to output NRSEs that uses
multiple motifs is:
getallNRSE.py
NRSE2.mot
NRSE2left.mot
NRSE2right.mot
findMotif.py 的輸出 以及 getallsites.py 的輸入均是 Cistematic .mot格式。
一個修飾的版本是getallsites.py 到 NRSEs 使用 多個 模體。
12.
The remaining scripts are just helper scripts to allow
comparison between runs and/or move data into UCSC format.
bedtoregion.py
makesitetrack.py
regiontobed.py
regionintersects.py
siteintersects.py
剩余的腳本是一些幫助腳本，幫助比較運行或轉(zhuǎn)換數(shù)據(jù)到UCSC格式
II. 程序測試實例.
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