Changes between Version 14 and Version 15 of SOP/PooledCRISPR

Timestamp:

11/24/20 15:36:20 (4 years ago)

Author:

byuan

Comment:

--

SOP/PooledCRISPR

@@ -50 +50 @@
 * See /nfs/BaRC_Public/BaRC_code/Perl/read_count_CRISPR_guides for this implementation.
 
-'''Implementation 2: using bowtie alignment'''
+'''Implementation 2: If you cannot access to the script in the above folder, you can use bowtie to do the alignment'''
 * Make bowtie index with sgRNA sequences, and ran bowtie to align reads to indexed sgRNAs.
 
@@ -86 +86 @@
 
 {{{
+
+# the options -t and -c specificity the treatment and control samples, respectively.
 mageck test -k count_matrix.txt -t top1,top2 -c bot1,bot2 -n mageck_out.txt
-# the options -t and -c specificity the treatment and control samples, respectively.
+
+# For paired samples:
+mageck test -k count_matrix.txt -t top1,top2 -c bot1,bot2 -n mageck_out.txt --paired
+
 }}}
 
@@ -106 +111 @@
 
 The output files include,
-  - .summary.pdf file which summarizes (only) the top hits, and also includes a waterfall plot.
+
   - .gene_summary.txt results summarized by gene (for all genes)
   - .sgrna_summary.txt resuls by guide (for all guides); this file can be made into a matrix using a few UNIX commands, e.g. 
 
+Run .Rmd to create a file (.summary.pdf) which summarizes (only) the top hits, and also includes a waterfall plot.
 
 {{{