Z******5
发帖数: 435 | 1 最近在做一个转录因子，发现UCSC上有ChIP-seq的数据，想弄下来做个全面分析。
现在能做到的是：从ftp上下载bigWig数据，然后用bwtool过滤，然后转成Wig格式，然
后再转成Bed格式，然互再提交到GREAT做分析。
问题是：过滤后的数据转为Bed有 300M 左右，但是GREAT只能提交50M且不超过50000个
element，这样上传的文件基本只有5M左右，或者更低。
请问有啥好办法能够一次性注释300M或者更大的Bed文件呀？ | g********6
发帖数: 86 | | s*********x
发帖数: 1923 | 3 download the peak file, rather the raw wig file. | Z******5
发帖数: 435 | 4 谢谢~~
【在 g********6 的大作中提到】
: 可以用Homer
| Z******5
发帖数: 435 | 5 Do you mean the the narrowPeak or broadPeak? here http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/
and here http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/
Two questions:
1. For examples, for a 2647 kb narrowPeak file with 45217 lines, the GREAT
still remained Error.
GREAT encountered a user error.
GREAT could not process your request. Please submit data via the GUI or
programming interface.
GREAT currently supports input files of up to 500,000 test regions and 1,000
,000 background regions, totalling no more than 50 MB in size, whichever is
more restrictive.
Please modify your data and re-submit it.
What limitations does GREAT have on input file sizes?
2. The narrowPeak file is a filtered file as compared to the bigWig file
with a definite threshold. I can't use a broad throld.
Thx
【在 s*********x 的大作中提到】
: download the peak file, rather the raw wig file.
| Z******5
发帖数: 435 | 6 The peak file is fine.
Thanks
【在 s*********x 的大作中提到】
: download the peak file, rather the raw wig file.
| j*p
发帖数: 411 | 7 Download the peak file, rank by intensity, use the top 10k or whatever for
GREAT. | m******5
发帖数: 1383 | 8 you may have some misunderstanding on what you are looking at.
judging by what you said, the Bed file you are trying to submit is actually
a bedgraph instead of a bed file containing a list of binding sites.
For analyzing using Great, you need a list of binding sites obtained from
peak calling.
To obtain such list, you can do peak calling directly using your bigwig file
by MACS2 or MACS.
【在 Z******5 的大作中提到】
: 最近在做一个转录因子，发现UCSC上有ChIP-seq的数据，想弄下来做个全面分析。
: 现在能做到的是：从ftp上下载bigWig数据，然后用bwtool过滤，然后转成Wig格式，然
: 后再转成Bed格式，然互再提交到GREAT做分析。
: 问题是：过滤后的数据转为Bed有 300M 左右，但是GREAT只能提交50M且不超过50000个
: element，这样上传的文件基本只有5M左右，或者更低。
: 请问有啥好办法能够一次性注释300M或者更大的Bed文件呀？
| Z******5
发帖数: 435 | 9 Yes, I was misdirected from the start.
I have finished it by using the narrowPeak file downloading from the UCSC
web site.
Now I'm learning MACS2, it's a very usefull tool. Thanks for your suggestion.
actually
file
【在 m******5 的大作中提到】
: you may have some misunderstanding on what you are looking at.
: judging by what you said, the Bed file you are trying to submit is actually
: a bedgraph instead of a bed file containing a list of binding sites.
: For analyzing using Great, you need a list of binding sites obtained from
: peak calling.
: To obtain such list, you can do peak calling directly using your bigwig file
: by MACS2 or MACS.
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