请教UCSC ChIP-seq数据的分析 - 未名空间MITBBS历史存档

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请教UCSC ChIP-seq数据的分析

请教UCSC ChIP-seq数据的分析# Biology - 生物学

A*g2015-05-31 07:05

1 楼

We mailed 485 and 765 (primary and spouse) to NSC on May 3, 2011. I can
checked it was dilieved on May 4, 2011. And we still didn't get any update
info, no recipe, no cash checked.
Am I mailed to wrong PO BOX? I mailed my EB1A 140 to NSC: For Form I-140
filed alone, mail the form to:
USCIS Nebraska Service Center
P.O. Box 87140
Lincoln, NE. 68501-7140.
For 485, I didn't know file to where, after reading the 140 instructions, I
filed it to the other box as:
For Form I-140 filed concurrently with Form I-485, Application to Register
Permanent Residence or Adjust Status, mail your forms package to:
USCIS Nebraska Service Center
P.O. Box 87485
Lincoln, NE. 68501-7485.
Did I mail wrong? Should I mail 485 exactly as I mailed 140? Than what
should I do? Mail again?
Please take a look and give me some suggestion!
Thank you all!

d*f2015-05-31 07:05

2 楼

当年偎身姐妹怀中的于小彤，如今身高蹿至1米9；当年清新可人的“小婉君”，一副夜
店扮相“烟熏妆”雷倒众评审……今晚《天声王牌》，众童星早已不是当年模样。
于小彤跨界冲关安徽卫视《天声王牌》。对于自己的身高给摄影师带来的不便，他乖巧
主动地劈腿装矮，完全不似当年那个因观众批评李少红而鲁莽伤人的小男孩。
如果说于小彤只是身高惊到大家，金铭则是全方位颠覆，不仅有熟女言谈，更以烟熏妆
夜店扮相雷倒《天声王牌》众评审。
金铭首支参赛曲目是她做童星时的代表作《青青河边草》，第二首歌明明也是一曲清纯
的《但愿人长久》，却被金铭演绎得宛如夜店《夜来香》。其烟熏妆更让众评审无语，
率真的孙悦实在按捺不住，明示金铭，“想转型可以，但也不能太过，不如等参加了《
天声王牌》之后，我教你。

Z*52015-05-31 07:05

3 楼

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？

A*g2015-05-31 07:05

4 楼

worry to cry, plese help me!

g*62015-05-31 07:05

5 楼

可以用Homer

s*t2015-05-31 07:05

6 楼

不懂，帮顶。
485的mailing address instruction 写很不清楚。bless

s*x2015-05-31 07:05

7 楼

download the peak file, rather the raw wig file.

y*u2015-05-31 07:05

8 楼

should be right. I sent to the same address NSC PO 87485 and they
transferred our cases to TSC. Waited almost a month to get the receipts.
Just relax.

I

【在 A***g 的大作中提到】

: We mailed 485 and 765 (primary and spouse) to NSC on May 3, 2011. I can
: checked it was dilieved on May 4, 2011. And we still didn't get any update
: info, no recipe, no cash checked.
: Am I mailed to wrong PO BOX? I mailed my EB1A 140 to NSC: For Form I-140
: filed alone, mail the form to:
: USCIS Nebraska Service Center
: P.O. Box 87140
: Lincoln, NE. 68501-7140.
: For 485, I didn't know file to where, after reading the 140 instructions, I
: filed it to the other box as:

Z*52015-05-31 07:05

9 楼

谢谢~~

【在 g********6 的大作中提到】

: 可以用Homer

s*t2015-05-31 07:05

10 楼

你的140是在TSC批的吗？

【在 y****u 的大作中提到】

: should be right. I sent to the same address NSC PO 87485 and they
: transferred our cases to TSC. Waited almost a month to get the receipts.
: Just relax.
:
: I

Z*52015-05-31 07:05

11 楼

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.

A*g2015-05-31 07:05

12 楼

It was approved at NSC.

【在 s*******t 的大作中提到】

: 你的140是在TSC批的吗？

Z*52015-05-31 07:05

13 楼

The peak file is fine.
Thanks

【在 s*********x 的大作中提到】

: download the peak file, rather the raw wig file.

A*g2015-05-31 07:05

14 楼

Oh, that make me feel better. Thank you!
But why transferred to TSC?

【在 y****u 的大作中提到】

: should be right. I sent to the same address NSC PO 87485 and they
: transferred our cases to TSC. Waited almost a month to get the receipts.
: Just relax.
:
: I

j*p2015-05-31 07:05

15 楼

Download the peak file, rank by intensity, use the top 10k or whatever for
GREAT.

m*n2015-05-31 07:05

16 楼

all these 485 based on an approved 140 should go to TSC dallas lockbox as
shown in USCIS website. but the reality is that some sent directly to NSC
also went through.

【在 A***g 的大作中提到】

: Oh, that make me feel better. Thank you!
: But why transferred to TSC?

m*52015-05-31 07:05

17 楼

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？

A*g2015-05-31 07:05

18 楼

Thank you for your reply.
Now I KNOW I should send it to TSC dallas lockbox. I checked the website a
lot of times before but I totally ignored that sentence. Oh, it's my own
fault ! I should be careful......

【在 m***n 的大作中提到】

: all these 485 based on an approved 140 should go to TSC dallas lockbox as
: shown in USCIS website. but the reality is that some sent directly to NSC
: also went through.

Z*52015-05-31 07:05

19 楼

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.