Changes between Version 5 and Version 6 of SOP/PooledCRISPR


Ignore:
Timestamp:
03/21/19 15:56:27 (6 years ago)
Author:
byuan
Comment:

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Legend:

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  • SOP/PooledCRISPR

    v5 v6  
    5353* Make bowtie index with sgRNA sequences, and ran bowtie to align reads to indexed sgRNAs.
    5454* Sample commands with 0 mismatch in the alignment
    55 ** bowtie-build guide.fa guide
    56 ** bowtie  -3 20 -n 0  -l 20 -p 4  -S guide foo.fq.gz foo.sam
     55* bowtie-build guide.fa guide
     56* bowtie  -3 20 -n 0  -l 20 -p 4  -S guide foo.fq.gz foo.sam
    5757
    58 *** -3: trim <int> bases from 3' end of reads
    59 *** -n: <int> max mismatches in seed (can be 0-3, default: -n 2)
    60 *** -l: <int> seed length for -n (default: 28)
    61 *** -p: <int> number of alignment threads to launch (default: 1)
     58* -3: trim <int> bases from 3' end of reads
     59* -n: <int> max mismatches in seed (can be 0-3, default: -n 2)
     60* -l: <int> seed length for -n (default: 28)
     61* -p: <int> number of alignment threads to launch (default: 1)
    6262
    6363