Haynes Lab:Notebook/Jan/2014/04/23: Difference between revisions
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|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">Using Public Data to Predict and Control Stem Cell Development</span> | |style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">Using Public Data to Predict and Control Stem Cell Development</span> | ||
|style="background-color: #F2F2F2" align="center"| | |style="background-color: #F2F2F2" align="center"|[[File:Report.png|frameless|link={{#sub:{{FULLPAGENAME}}|0|-11}}]][[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|[[File:Resultset_previous.png|frameless|link={{#lnpreventry:{{FULLPAGENAME}}}}]][[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]] }}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]][[File:Resultset_next.png|frameless|link={{#lnnextentry:{{FULLPAGENAME}}}}]]}} | ||
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#To add a track that contains the chromatin mapping data of interest, set group to Regulation, and track to a type of interest. For instance, try Broad Histone or UW Histone to analyze a histone mark. | #To add a track that contains the chromatin mapping data of interest, set group to Regulation, and track to a type of interest. For instance, try Broad Histone or UW Histone to analyze a histone mark. | ||
#On the region line, click the “define regions” button. In the text window, paste in the text below (tab-delimited), then click the “submit” button. | #On the region line, click the “define regions” button. In the text window, paste in the text below (tab-delimited), then click the “submit” button. | ||
chr7 5569982 | chr7 5569982 5570482 ACTB <br /> | ||
chr3 52231849 52232349 ALAS1 | chr3 52231849 52232349 ALAS1 <br /> | ||
chr15 45003435 45003935 B2M | chr15 45003435 45003935 B2M <br /> | ||
chrX 153774983 153775483 G6PD | chrX 153774983 153775483 G6PD <br /> | ||
chr12 6643335 6643835 GAPDH | chr12 6643335 6643835 GAPDH <br /> | ||
chr7 65447051 65447551 GUSB | chr7 65447051 65447551 GUSB <br /> | ||
chrX 133593925 133594425 HPRT1 | chrX 133593925 133594425 HPRT1 <br /> | ||
chrX 77359416 77359916 PGK1 | chrX 77359416 77359916 PGK1 <br /> | ||
chr7 44835991 44836491 PPIA | chr7 44835991 44836491 PPIA <br /> | ||
chr6 170863171 170863671 TBP | chr6 170863171 170863671 TBP <br /> | ||
chr1 212738426 212738926 ATF3 | chr1 212738426 212738926 ATF3 <br /> | ||
chr12 4382652 4383152 CCND2 | chr12 4382652 4383152 CCND2 <br /> | ||
chr9 21974882 21975382 CDKN2A | chr9 21974882 21975382 CDKN2A <br /> | ||
chr2 38303073 38303573 CYP1B1 | chr2 38303073 38303573 CYP1B1 <br /> | ||
chr4 107957203 107957703 DKK2 | chr4 107957203 107957703 DKK2 <br /> | ||
chr7 27224585 27225085 HOXA11 | chr7 27224585 27225085 HOXA11 <br /> | ||
chr16 56701727 56702227 MT1G | chr16 56701727 56702227 MT1G <br /> | ||
chr20 62795577 62796077 MYT1 | chr20 62795577 62796077 MYT1 <br /> | ||
chr21 34397966 34398466 OLIG2 | chr21 34397966 34398466 OLIG2 <br /> | ||
chr3 25469584 25470084 RARB | chr3 25469584 25470084 RARB <br /> | ||
#Set output format as “selected fields from primary and related tables.” Click the get output button. | #Set output format as “selected fields from primary and related tables.” Click the get output button. | ||
#On the proceeding “Select Fields” page, select chrom, chromStart, chromEnd, name, and signalValue. Click the get output button. The output will be the coordinates of signalValues (from the track, from step 3) that fall within the regions of interest (from step 4). Note: coordinates for which the chromatin-mapping signalValue is zero will be absent from the output list. | #On the proceeding “Select Fields” page, select chrom, chromStart, chromEnd, name, and signalValue. Click the get output button. The output will be the coordinates of signalValues (from the track, from step 3) that fall within the regions of interest (from step 4). Note: coordinates for which the chromatin-mapping signalValue is zero will be absent from the output list. | ||
* The obtained table should look something like this: | |||
chrom chromStart chromEnd name signalValue <br /> | |||
chr15 44997836 45024078 . 2.89004 <br /> | |||
chr15 45002305 45003965 . 12.4601 <br /> | |||
chr15 45003383 45003505 . 12.452 <br /> | |||
chr12 6643737 6645039 . 3.11452 <br /> | |||
chrX 77356139 77365636 . 1.90484 <br /> | |||
chr12 4369203 4402228 . 2.29872 <br /> | |||
chr2 38303256 38304176 . 16.0045 <br /> | |||
chr16 56252416 58646068 . 1.57571 <br /> | |||
Latest revision as of 23:55, 26 September 2017
Using Public Data to Predict and Control Stem Cell Development | Main project page Previous entry Next entry |
Preliminary Analysis: Using the UCSC Genome Browser and ENCODE Data
chr7 5569982 5570482 ACTB
chrom chromStart chromEnd name signalValue
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