Changes between Version 8 and Version 9 of SOP/PooledCRISPR

Timestamp:

03/21/19 16:03:38 (6 years ago)

Author:

byuan

Comment:

--

SOP/PooledCRISPR

@@ -53 +53 @@
 * Make bowtie index with sgRNA sequences, and ran bowtie to align reads to indexed sgRNAs.
 
-* Sample commands with 0 mismatch in the alignment:
+* Sample commands with 0 mismatch in the alignment, with 20bp long sequence
 * bowtie-build guide.fa guide
 * bowtie  -3 20 -n 0  -l 20 -p 4  -S guide foo.fq.gz foo.sam
@@ -64 +64 @@
 * Note: don't use --best nor -m with bowtie
 
+* Command to assign read counts for each sgRNA:
+* grep -v ^\@ foo.sam | awk -F"\t" '{ if($2==0 && $13=="MD:Z:20") print $3 }' |sort |uniq -c |awk '{ print $2"\t"$1 }' 
 
-