Changes between Version 7 and Version 8 of SOPs/Using


Ignore:
Timestamp:
04/28/22 15:33:42 (3 years ago)
Author:
thiruvil
Comment:

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  • SOPs/Using

    v7 v8  
    22
    33[[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.
    4 The regions used can be genes included on the ngsplot annotation or custom regions included on a bed file.
     4The regions used can be genes included on the ngsplot annotation or custom regions included on a bed file. 
    55
    66* Here is an example of a ngsplot command using custom regions
     7
    78{{{
    89bsub ngs.plot.r -G hg19 -R bed -L 3000 -C config.txt -O Peak_Summits
    … …  
    1415Pol2.sorted.bam   peaks.SUMMIT.bed      "Pol2"
    1516}}}
     17
    1618* Here is an example of a ngsplot command using gene annotations within the ngsplot package
    1719
    … …  
    3133See [[https://github.com/shenlab-sinai/ngsplot/wiki/HowAreYaxisValsCalculated | ngsplot: how the Y-axis values are calculated]].
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    33