question: how to make the CHIP-seq txt data more visible

Question

[guguangxiang]

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

[jotan]

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?

[guguangxiang]

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.

[jotan]

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