Changes between Version 9 and Version 10 of SOPs/qc_shortReads

Timestamp:

12/03/13 10:27:21 (11 years ago)

Author:

byuan

Comment:

--

SOPs/qc_shortReads

@@ -53 +53 @@
    hist(distance, breaks=200, col="wheat", main=paste("Insert sizes for", sample.name), xlab="length (nt)")
    dev.off()
+}}}
+{{{
+   # calculate insert size with CollectInsertSizeMetrics function from picard ( http://picard.sourceforge.net )
+   # 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
 }}}