Dear Sir/Madam,
I am trying to use the human CHIP-seq data on UCSC and now I have
several questions about it.
From the hg19 browser page, the only one chip-seq data in the regulation
tracks is the "ENCODE regulation tracks", which includes the "Txn Factor ChIP"
track. However, from the Table browser download page, we can find several other
CHIP TFBS tracks, such as HAIB TFBS and UTA TFBS etc.
Is it because that the Txn Factor ChIP track includes all the data of
others? So if I need the most comprehensive CHIP data, should I donwload only
the Txn Factor ChIP track data or also download other TFBS data in the table
browser page?
I noticed that one track has many experiments for the same TF, such as
for the Nrsf TF in the HAIB TFBS track, there are the following experiments.
For these, should I use the intersection data to reduce false positve for the
Nrsf tfbs?
wgEncodeHaibTfbsGm12878NrsfPcr2xPkRep1.broadPeak
wgEncodeHaibTfbsGm12878NrsfPcr2xPkRep2.broadPeak
wgEncodeHaibTfbsH1hescNrsfV0416102PkRep1.broadPeak
wgEncodeHaibTfbsH1hescNrsfV0416102PkRep2.broadPeak
wgEncodeHaibTfbsHelas3NrsfPcr1xPkRep1.broadPeak
wgEncodeHaibTfbsHelas3NrsfPcr1xPkRep2.broadPeak
wgEncodeHaibTfbsHepg2NrsfPcr2xPkRep1.broadPeak
wgEncodeHaibTfbsHepg2NrsfPcr2xPkRep2.broadPeak
wgEncodeHaibTfbsK562NrsfV0416102PkRep1.broadPeak
wgEncodeHaibTfbsK562NrsfV0416102PkRep2.broadPeak
wgEncodeHaibTfbsPanc1NrsfPcr2xPkRep1.broadPeak
wgEncodeHaibTfbsPanc1NrsfPcr2xPkRep2.broadPeak
wgEncodeHaibTfbsPfsk1NrsfPcr2xPkRep1.broadPeak
wgEncodeHaibTfbsPfsk1NrsfPcr2xPkRep2.broadPeak
wgEncodeHaibTfbsSknshNrsfPcr2xPkRep1.broadPeak
wgEncodeHaibTfbsSknshNrsfPcr2xPkRep2.broadPeak
wgEncodeHaibTfbsU87NrsfPcr2xPkRep1.broadPeak
wgEncodeHaibTfbsU87NrsfPcr2xPkRep2.broadPeak
For the conserved TFBS prediction in the "TFBS Conserved" track, I noticed
ther are much more data than the data downloaded from hg18 previously. However,
the description page of this track
(http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=255151677&c=chr21&g=tfbsConsSites),
it seem no different from the hg18 page, which said using the TransFac 7.0
matrix and the same program. If that, why much more tfbs were predicted? I
guess you use the new version of TransFac matrix but didn't update the
description page, right?
These data are very important for us. I am looking forward for your reply.
Thanks very much.
Best,
Anyuan Guo
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
