Changes between Version 15 and Version 16 of SOPs/qc_shortReads

Timestamp:

01/30/14 13:17:50 (11 years ago)

Author:

gbell

Comment:

--

SOPs/qc_shortReads

@@ -33 +33 @@
 
 
-== QC Paired-End Reads ==
+== QC for paired-end reads ==
   * QC as above each of the forward and reverse reads separately using QC'ing program (above).
   * If reads reads are removed, get reads/mates after QC'ing that are //perfect// pairs: 
@@ -41 +41 @@
 }}}
 
-  * '''Paired-End Insert Size for DNA samples''': If 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.  See the [[http://barcwiki.wi.mit.edu/wiki/SOPs/mapping|mapping SOP]] for mapping details.
-
-{{{
-   # Map with bowtie (or another mapper)
-   bowtie -S /nfs/genomes/mouse_gp_jul_07/bowtie/mm9 -1 s_1_1_sequence.txt -2 s_1_2_sequence.txt -n 1 -p 2 -I 0 -X 500 >| s_1_bowtie.sam
-}}}
+== Determining the paired-end insert size for DNA samples ==
+
+If 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.  
+
+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.
+
 
 Method 1: Get insert sizes from BAM file