Changes between Version 3 and Version 4 of SOPs/qc_shortReads

Timestamp:

09/11/13 15:12:20 (11 years ago)

Author:

gbell

Comment:

--

SOPs/qc_shortReads

@@ -27 +27 @@
   * If reads reads are removed, get reads/mates after QC'ing that are //perfect// pairs: 
 
- {{{
-    bsub “perl /nfs/BaRC_Public/BaRC_code/Perl/cmpfastq/cmpfastq.pl s_8_1_sequence.txt s_8_2_sequence.txt”
-}}}
-
-  * '''Paired-End Insert Size''': 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.
-
- {{{
-    # Run bowtie
-    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
+{{{
+   bsub “perl /nfs/BaRC_Public/BaRC_code/Perl/cmpfastq/cmpfastq.pl s_8_1_sequence.txt s_8_2_sequence.txt”
+}}}
+
+  * '''Paired-End Insert Size''': 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 more 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
 }}}
 
@@ -61 +61 @@
   * QC a single file using ShortRead
 
- {{{
+{{{
    library("ShortRead")
-    # load the data
-    sr <- readFastq("s1_sequence.txt")
-    # create a qa object from the ShortRead object
-    qa <- qa( sr, lane="character" )
-    # create an html report in the qa directory
-    report(qa, dest="my_qa")
-
-  * QC all *.txt fastq files in a directory using ShortRead
-
-    library("ShortRead")
-    qaSummary <- qa(".", pattern="*.txt", type="fastq")
-    #create an html report in the qa directory
-    report(qaSummary, dest="myQC_dir")  
+   # load the data
+   sr <- readFastq("s1_sequence.txt")
+   # create a qa object from the ShortRead object
+   qa <- qa( sr, lane="character" )
+   # create an html report in the qa directory
+   report(qa, dest="my_qa")
+}}}
+
+  * QC all *.txt fastq files in a directory using ShortRead.
+
+{{{
+   library("ShortRead")
+   qaSummary <- qa(".", pattern="*.txt", type="fastq")
+   #create an html report in the qa directory
+   report(qaSummary, dest="myQC_dir")  
 }}}
 
@@ -83 +85 @@
  
 {{{
-  # sample commands: 
+   # Sample commands: 
    # quality_stats: Sampl Solexa reads file: s_1_1_sequence.txt
    fastx_quality_stats -i s_1_1_sequence.txt -o s_1_1_sequence.stats