User:Karmella Haynes/Notebook/PcTF Genomics/2013/01/07: Difference between revisions
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|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">Pc-TF Genomics</span> | |style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">Pc-TF Genomics</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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## Configure Advanced Options: under Peak Detection, is set to Qseq Peak Finder by default. Leave this as-is for now. | ## Configure Advanced Options: under Peak Detection, is set to Qseq Peak Finder by default. Leave this as-is for now. | ||
## Click [Next >]. Wait a while | ## Click [Next >]. Wait a while | ||
# | # Setup Attributes and Replicates: Show only grouping attributes (default). Click [Finish]. | ||
# Window with Peak Table and other tabs should appear. Finished! Explore the data. | |||
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* Set control 2_ and 7_aln_sorted as "yes" for "Is control?" | * Set control 2_ and 7_aln_sorted as "yes" for "Is control?" | ||
* Set 2_aln_sorted as control for 1_aln_sorted. Set 7_aln_sorted as control for 6_aln_sorted. | * Set 2_aln_sorted as control for 1_aln_sorted. Set 7_aln_sorted as control for 6_aln_sorted. | ||
* <font color="red">This analysis required too much disk space</font> | ** <font color="red">This analysis required too much disk space</font> | ||
* Started over, but only used chromosomes 1-3 as reference templates (trying a few at a time). | * Started over, but only used '''chromosomes 1-3''' as reference templates (trying a few at a time). | ||
** This worked | |||
Results/ Notes: | |||
* Peak Table: shows very few hits for PcTF, many more for H3K27me3, no overlap! | |||
* Display wig file on UCSC Genome browser online - add file from "ChIPseq Wig Files" folder as a custom track; wig file shows raw data histogram | |||
** 1_aln_sorted.wig, 6_aln_sorted.wig | |||
* Display BED file on UCSC Genome browser online - add file from "ChIPseq BED Files" folder as a custom track; BED file shows | |||
** 1_aln_sorted.bed, 6_aln_sorted.bed | |||
Latest revision as of 22:20, 26 September 2017
Pc-TF Genomics | Main project page Previous entry Next entry |
01/07/13
Array Star analysis
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