Changes between Version 16 and Version 17 of SOPs/miningSAMBAM

Timestamp:

06/03/14 15:03:54 (11 years ago)

Author:

thiruvil

Comment:

--

SOPs/miningSAMBAM

@@ -1 @@
-== Mining, summarizing, and processing SAM/BAM files ==
+== Summarizing, processing and quality control(QC) of SAM/BAM files ==
 
 Many of these involve [http://samtools.sourceforge.net/samtools.shtml | samtools]
@@ -86 +86 @@
 
 
-=== Use QualiMap to get (visual) summary of mapping statistics eg. coverage/distribution ===
+=== Get a list of multi-mapped reads, including the number of times each one was mapped ===
+
+Tophat/bowtie mappers create the tag NH:i:XXX where XXX is the number of times the read has mapped.
+{{{
+bsub "samtools view accepted_hits.bam | grep -v NH:i:1 | perl -pe 's/AS.+(NH:i:\d+)/\$1/' | cut -f1,10,12 | perl -pe 's/NH:i://' | sort -u -k3,3nr > Multi-mapped.sorted.txt"
+# Output format:
+# read_ID<tab>read<tab>number times mapped
+}}}
+
+=== QC to get a (visual) summary of mapping statistics.  For eg. coverage/distribution of mapped reads across the genome or transcriptome. ===
+
+==== RSeQC: RNA-Seq quality control package ====
+{{{
+#get mapping statistics (eg. unique/multi-mapped reads)
+bam_stat.py -i myFile.bam
+}}}
+
+==== QualiMap: can be used on DNA or RNA-Seq ====
 {{{
 # Graphical interface: enter 'qualimap' on the command line
@@ -95 +112 @@
 bsub "qualimap rnaseq -bam myFile.bam -gtf Homo_sapiens.GRCh37.72.canonical.gtf -outdir output_qualimap_rnaseq -protocol non-strand-specific"
 }}}
-
-=== Get a list of multi-mapped reads, including the number of times each one was mapped ===
-
-Tophat/bowtie mappers create the tag NH:i:XXX where XXX is the number of times the read has mapped.
-{{{
-bsub "samtools view accepted_hits.bam | grep -v NH:i:1 | perl -pe 's/AS.+(NH:i:\d+)/\$1/' | cut -f1,10,12 | perl -pe 's/NH:i://' | sort -u -k3,3nr > Multi-mapped.sorted.txt"
-# Output format:
-# read_ID<tab>read<tab>number times mapped
-}}}