Changes between Version 20 and Version 21 of SOPs/SAMBAMqc


Ignore:
Timestamp:
04/26/17 11:18:25 (8 years ago)
Author:
gbell
Comment:

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  • SOPs/SAMBAMqc

    v20 v21  
    1717If paired-end insert size or distance is unknown or need to be verified, it can be extracted from a BAM/SAM file after running Bowtie. 
    1818
    19 When mapping with bowtie (or another mapper), the insert size can often be included as an input parameter (example for bowtie: -X 500), which can help with mapping.  See the [[http://barcwiki.wi.mit.edu/wiki/SOPs/mapping mapping SOP]] for mapping details.
    20 
     19When mapping with bowtie (or another mapper), the insert size can often be included as an input parameter (example for bowtie: -X 500), which can help with mapping. 
     20See our [http://barcwiki.wi.mit.edu/wiki/SOPs/mapping  mapping SOP] for mapping details.
    2121
    2222Method 1: Get insert sizes from BAM file
    … …  
    196196== Interpreting quality control issues ==
    197197
    198 See [[https://sequencing.qcfail.com/ QCFAIL.com]] from the Babraham Institute
     198See [https://sequencing.qcfail.com/ QCFAIL.com] from the Babraham Institute
    199199
    200200\\