User:Karmella Haynes/Notebook/PcTF Genomics/2014/07/23: Difference between revisions
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== | ==07/23/14== | ||
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* | * ChIPseq - bioinformatics | ||
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* Found free promoters database at the Eukaryotic Promoter Database website | * Found free promoters database at the Eukaryotic Promoter Database website | ||
* Retrieved BED file of all human promoters from: http://epd.vital-it.ch/get_promoters.php | * Retrieved BED file of all human promoters from: http://epd.vital-it.ch/get_promoters.php | ||
** Selected H. sapiens, left all other options blank, clicked [select], downloaded BED file, uploaded to Galaxy | ** Selected H. sapiens, left all other options blank, clicked [select], downloaded BED file, uploaded to Galaxy as Promoters EPD All | ||
** Total promoters: 23,316 | ** Total promoters: 23,316 | ||
** Each is only 10 bp long | |||
** Gene names are included! | ** Gene names are included! | ||
* Note: Custom-generated promoter file (500 bp TSS regions) = 26,960. This is over 3k more than the EPD. | |||
'''New Galaxy files'''<br> | |||
Note: EPD allows selection of promoter sub-classes | |||
** All EPD promoters - uploaded as Promoters EPD All | |||
** TATA-box motif - Promoters EPD TATA = 2,007 regions | |||
** Initiator motif - Promoters EPD Init = 6,538 regions | |||
** CCAAT-box motif - Promoters EPD CCAAT = 3,838 regions | |||
** GC-box motif - Promoters EPD GC = 10,695 regions | |||
** CpG (unable to retrieve...looks like criteria have not been added yet) | |||
Revision as of 15:28, 23 July 2014
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07/23/14
Promoters research
New Galaxy files
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