Question: question: how to make the CHIP-seq txt data more visible
0
gravatar for guguangxiang
4.3 years ago by
United States
guguangxiang0 wrote:

Hi:

I am a new person here. I find some chip-seq data from GEO database, it is showed as below. want to know how to make the data more visible.  like some chip-seq data shown in IGV?  Thanks.

#PeakID chr start end strand Normalized Tag Count focus ratio findPeaks Score Fold Change vs Local p-value vs Local Clonal Fold Change
chr2-1 chr2 98507048 98507548 + 4684 0.671 1796 14.57 0.00E+00 0.28
chr2-2 chr2 98502596 98503096 + 2071.2 0.59 782 4.52 1.74E-249 0.51
chr9-1 chr9 35112734 35113234 + 1540.1 0.621 580 612.22 0.00E+00 0.59
chr12-1 chr12 3109721 3110221 + 1165.7 0.862 440 556.07 0.00E+00 0.67
chr9-2 chr9 3000164 3000664 + 653.2 0.69 258 8.87 1.17E-140 0.79
chr6-1 chr6 103598962 103599462 + 520.4 0.959 196 338.55 0.00E+00 0.83
chr15-1 chr15 74917046 74917546 + 493.9 0.56 186 22.23 1.30E-175 0.84
chrUn_random-1 chrUn_random 5495590 5496090 + 398.3 0.741 150 13.38 7.11E-111 0.86
chip-seq • 1.0k views
ADD COMMENTlink modified 4.3 years ago by jotan1.2k • written 4.3 years ago by guguangxiang0

This a list of peaks, not a ChIP-seq track. Could you post an example of what you mean by ChIP-seq data shown in IGV?

ADD REPLYlink written 4.3 years ago by jotan1.2k

Hi jotan:

I do not know what is the meaning of "not chip-seq track", I downloaded the data from geo database, and it should be Chip-seq data, but has been analysed by the author. The data are shown in a picture in IGV, and can be searched by gene symbols. I do not know how to show the picture here. Thanks.

ADD REPLYlink modified 3 months ago by RamRS25k • written 4.3 years ago by guguangxiang0

Here is an example of a peak track and its corresponding sequencing track viewed in UCSC

The top gray blocks are a list of peak coordinates, similar to what you have in your example.

The blue track underneath is a representation of sequencing reads.

It is commonly stored as a wig/big wig file

http://genome.ucsc.edu/goldenPath/help/wiggle.html

ADD REPLYlink modified 3 months ago by RamRS25k • written 4.3 years ago by jotan1.2k
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