Changes between Version 11 and Version 12 of SOPs/qc_shortReads

Timestamp:

12/03/13 11:07:32 (11 years ago)

Author:

gbell

Comment:

--

SOPs/qc_shortReads

@@ -56 +56 @@
 }}}
 
-Method 2: Calculate insert sizes with CollectInsertSizeMetrics function from picard ( http://picard.sourceforge.net )
+Method 2: Calculate insert sizes with CollectInsertSizeMetrics function from picard (http://picard.sourceforge.net).  This is also a good approximation for RNA samples.
 {{{
    # 
-   # I=File    Input SAM or BAM file.  Required.
-   # O=File    File to write the output to.  Required
-   # R=File    Reference sequence fasta
-   # H=File    File to write insert size histogram chart to  Required.
-   # output: CollectInsertSizeMetrics.txt: values for -r and --mate-std-dev cna be found in this text file
-   #         CollectInsertSizeMetrics_hist.pdf: graphic representation of the insert
-bsub java -jar  /usr/local/share/picard-tools/CollectInsertSizeMetrics.jar I=foo.bam O=CollectInsertSizeMetrics.txt H=CollectInsertSizeMetrics_hist.pdf R=/nfs/genomes/mouse_gp_jul_07_no_random/fasta_whole_genome/mouse_all_no_random.fa
+   # I=File    Input SAM or BAM file.  (Required)
+   # O=File    File to write the output to.  (Required)
+   # H=File    File to write insert size histogram chart to.  (Required)
+   # output: CollectInsertSizeMetrics.txt: values for -r and --mate-std-dev can be found in this text file
+   #         CollectInsertSizeMetrics_hist.pdf: insert size histogram (graphic representation)
+bsub java -jar  /usr/local/share/picard-tools/CollectInsertSizeMetrics.jar I=foo.bam O=CollectInsertSizeMetrics.txt H=CollectInsertSizeMetrics_hist.pdf
 }}}