Changes between Version 5 and Version 6 of SOPs/Using

Timestamp:

09/21/20 16:43:04 (4 years ago)

Author:

gbell

Comment:

--

SOPs/Using

@@ -1 +1 @@
 == Using ngsplot to make stacked heatmaps and profiles of genes or genomic regions (like ChIP-seq peaks) ==
- [[https://github.com/shenlab-sinai/ngsplot/wiki | ngsplot]] is a great tool to make heatmaps and profiles of mapped reads (i.e. bam files of RNA-seq, ChIP-seq etc) across genes, transcription starts sites or other regions of interest.
- The regions used can be genes included on the ngsplot annotation or custom regions included on a bed file.
+
+[[https://github.com/shenlab-sinai/ngsplot/wiki | ngsplot]] is a great tool to make heatmaps and profiles of mapped reads (i.e. bam files of RNA-seq, ChIP-seq etc) across genes, transcription starts sites or other regions of interest.
+The regions used can be genes included on the ngsplot annotation or custom regions included on a bed file.
 
 * Here is an example of a ngsplot command using custom regions
 {{{
-        bsub ngs.plot.r -G hg19 -R bed -L 3000 -C config.txt -O Peak_Summits
+bsub ngs.plot.r -G hg19 -R bed -L 3000 -C config.txt -O Peak_Summits
 
-        * Example of the tab delimited config.txt file
+using this example of the tab delimited config.txt file:
 
-         TF1.sorted.bam       peaks.SUMMIT.bed  "TF1" 
-         TF2.sorted.bam       peaks.SUMMIT.bed  "TF2" 
-         Pol2.sorted.bam      peaks.SUMMIT.bed  "Pol2" 
+TF1.sorted.bam    peaks.SUMMIT.bed      "TF1" 
+TF2.sorted.bam    peaks.SUMMIT.bed      "TF2" 
+Pol2.sorted.bam   peaks.SUMMIT.bed      "Pol2" 
 }}}
 * Here is an example of a ngsplot command using gene annotations within the ngsplot package
 
 {{{
-#using transcription start sites (tss)
+# Using transcription start sites (tss) as the features of interest
 bsub ngs.plot.r -G hg19 -R tss -L 3000 -C config.txt -O ngsplot_tss
 
-#using gene body
+# Using gene bodies as the features of interest
 bsub ngs.plot.r -G hg19 -R genebody -L 3000 -C config.txt -O ngsplot_tss
 
 }}}
 
-ngsplot uses a two-step normalization: i) coverage vectors' length i.e. gene length and ii) library size.
-[[https://github.com/shenlab-sinai/ngsplot/wiki/HowAreYaxisValsCalculated | ngsplot: How Are Y-axis Vals Calculated]]
+ngsplot uses a two-step normalization: i) coverage vectors' length i.e., gene length and ii) library size.
+See [[https://github.com/shenlab-sinai/ngsplot/wiki/HowAreYaxisValsCalculated | ngsplot: how the Y-axis values are calculated]].