Changes between Version 4 and Version 5 of SOP/PooledCRISPR

Timestamp:

03/21/19 15:55:45 (6 years ago)

Author:

byuan

Comment:

--

SOP/PooledCRISPR

@@ -51 +51 @@
 
 '''Implementation 2: using bowtie alignment'''
+* Make bowtie index with sgRNA sequences, and ran bowtie to align reads to indexed sgRNAs.
+* Sample commands with 0 mismatch in the alignment
+** bowtie-build guide.fa guide
+** bowtie  -3 20 -n 0  -l 20 -p 4  -S guide foo.fq.gz foo.sam
+
+*** -3: trim <int> bases from 3' end of reads
+*** -n: <int> max mismatches in seed (can be 0-3, default: -n 2)
+*** -l: <int> seed length for -n (default: 28)
+*** -p: <int> number of alignment threads to launch (default: 1)
 
 
+