Regions missing in track Transcription Factor ChIP-seq (161 factors) from ENCODE with Factorbook Motifs
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Santagostino Marco
Jul 20, 2016, 10:45:57 AM7/20/16
to gen...@soe.ucsc.edu
Dear Sir/Madam,
I used the track "Transcription Factor ChIP-seq (161 factors) from ENCODE with Factorbook Motifs" to investigate some regions of interest. I noticed that, among 19 regions, only 7 produced some result using Table Browser.
Why? is that a matter of stringency applied during the production of the data? These are regions corresponding to segmental duplication, might be an error related to their "condition"?
Thank you,
Regards,
Marco Santagostino
Marco Santagostino, PhD
Laboratorio di Biologia Molecolare e Cellulare
Dipartimento di Biologia e Biotecnologie, University of Pavia
Via Ferrata, 9 - 27100 Pavia, Italy
Laboratorio di Biologia Molecolare e Cellulare
Dipartimento di Biologia e Biotecnologie, University of Pavia
Via Ferrata, 9 - 27100 Pavia, Italy
Post Box: Via Ferrata, 1 - 27100 Pavia, Italy
Tel.: +39 0382 985540
Fax: +39 0382 528496
e-mail: marco.san...@unipv.it
Tel.: +39 0382 985540
Fax: +39 0382 528496
e-mail: marco.san...@unipv.it
Matthew Speir
Jul 22, 2016, 7:59:01 PM7/22/16
to Santagostino Marco, gen...@soe.ucsc.edu
Hi Marco,
Thank you for your question about the track "Transcription Factor ChIP-seq (161 factors) from ENCODE with Factorbook Motifs" in the UCSC Genome Browser.
Have you looked at these regions where there was no output in the Genome Browser? Are there entries for this track in that region? If the track does not have data at these positions in the Genome Browser, then nothing can be output from the Table Browser.
If there are regions that appear to be missing output when some should be expected, can you provide me with a few examples of these here? You can send your response to genom...@soe.ucsc.edu if you do not want to share this information with the public list.
Additionally, you can refer to the track description page for more information about how this track was produced: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
Thank you for your question about the track "Transcription Factor ChIP-seq (161 factors) from ENCODE with Factorbook Motifs" in the UCSC Genome Browser.
Have you looked at these regions where there was no output in the Genome Browser? Are there entries for this track in that region? If the track does not have data at these positions in the Genome Browser, then nothing can be output from the Table Browser.
If there are regions that appear to be missing output when some should be expected, can you provide me with a few examples of these here? You can send your response to genom...@soe.ucsc.edu if you do not want to share this information with the public list.
Additionally, you can refer to the track description page for more information about how this track was produced: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
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