Changes between Version 6 and Version 7 of SOPs/InProgressChipSeq


Ignore:
Timestamp:
05/14/14 15:54:07 (11 years ago)
Author:
ibarrasa
Comment:

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  • SOPs/InProgressChipSeq

    v6 v7  
    3737  * MACS may have trouble with a SAM file from bowtie if it contains unmapped reads (which it generally does).  As a result, you may need to filter out unmapped reads with a command like
    3838{{{
    39 samtools view -hS -F 4 s8_control_mouse_mm9.k1.n2.l36.best.sam > s8_control_mouse_mm9.k1.n2.l36.best.mapped_only.sam
    40 }}}
     39samtools view -hS -F 4 all_reads.sam > mapped_reads.sam
     40}}}
     41
    4142
    4243[[http://liulab.dfci.harvard.edu/MACS/|MACS]] ([[http://liulab.dfci.harvard.edu/MACS/00README.html|README]]) ([[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Search&db=pubmed&term=18798982|Zhang et al., 2008]])[[br]][[br]]