Changes between Version 1 and Version 2 of SOPs/InProgressChipSeq


Ignore:
Timestamp:
05/14/14 11:45:11 (11 years ago)
Author:
ibarrasa
Comment:

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  • SOPs/InProgressChipSeq

    v1 v2  
    1313
    1414 * See the [[http://barcwiki.wi.mit.edu/wiki/SOPs/mapping|mapping SOP]] for more details.
    15 
    16 === Step 2: Call peaks (bound regions) ===
     15=== Step 2: Calculate strand cross correlation ===
     16{{{
     17Rscript /nfs/BaRC_Public/phantompeakqualtools/run_spp.R -c=TreatmentIP.bam -savp -out=TreatmentIP.run_spp.out
     18}}}
     19
     20
     21=== Step 3: Call peaks (bound regions) ===
    1722Some of the parameters to consider when comparing programs are:
    1823  * Adjustment of sequence tags to better represent the original DNA fragment (by shifting tags in the 3′ direction or by extending tags to the estimated length of the original fragments)