How to View Peaks from ChIP-seq Data generated using old reference genome (hg18)

Question

[DareDevil]

I downloaded chiseq data from below link GSE25769. How do I use this data for viewing the peaks. The data analysis was performed using old reference genome hg18. What are the values in the column 2, 5, 7 represents?

Below is the information by running zcat GSM632892_HCT405_realign.txt.gz | head

#RUN_TIME Wed Oct  8 13:51:55 2008
#SOFTWARE_VERSION @(#) $Id: qualityFilter.pl,v 1.8 2007/11/26 14:42:26 tc Exp $
#FILTER_CRITERION ((CHASTITY>=0.6))
GGAATGGAATGGAATGGAATGGAACAACCCGAATGG 15906 1 ref_chr4:49347516 F GGAATGGAATGGAATGGAATGGATCAACCCGAGTGG 15906
GAACTTGATTTAAAATAATGTTGTATGTAGTATTTA 18000 1 ref_chr4:133533796 F GAACTTGATTTAAAATAATGTTGTATGTAGTATTTA 14859
GGACTAAGAATTGGGAGTACCCAGGACATCCAATTA 18000 8
GTCTTAGGCACAGTAATCAAGGAACCTAAGACCGAG 18000 1 ref_chr1:84351102 F GTCTTAGGCACAGTAATCAAGGAACCTAAGACCGAG 14859
GCAAAGACAAAAATCTTTCTAAGATTGGCCAAAATG 18000 1 ref_chr4:23417003 F GCAAAGACAAAAATCTTTCTAAGATTGGCCAAAATG 14859
GAAGTGCAGTGGTGGGATCTTGGCTCACTGCAAACT 18000 9
GGAAGGAGAGAAGAGATTGTAATAGAAATTAACAAT 18000 1 ref_chr17:64738595 R ATTGTTAATTTCTATTACAATCTCTTCTCTCCTTCC 14859

Also posted on SE Bioinformatics.

[ATpoint]

Honestly, download the fastq files and process yourself. Nothing gained by using legacy genomes and formats that are not standard today.

[DareDevil]

the raw fastq files for this data is not available

[ATpoint]

Then intrinsically the entire analysis and conclusions are not reproducible. I personally would never touch such a dataset.

[Kevin Blighe]

This is quite dismissive, and non-scientific.

[ATpoint]

That having, said by years of experience with ChIP-seq I can confidently say that it is a noisy assay that requires appropriate controls and replication. Without raw data, and with just these tables at hand, unclear how they were created, I think you are just building on uncertainty. Not worth it imo. Rather check whether there are other datasets available.