Changes between Initial Version and Version 1 of SOPs/miningSAMBAM

Timestamp:

01/23/13 16:49:43 (12 years ago)

Author:

trac

Comment:

--

SOPs/miningSAMBAM

@@ +1 @@
+== Mining, summarizing, and processing SAM/BAM files ==
+
+Many of these involve [http://samtools.sourceforge.net/samtools.shtml | samtools]
+
+=== Convert, sort, and/or index ===
+
+
+{{{
+Convert SAM to BAM:
+ samtools view -bS -o foo.bam foo.sam
+}}}
+
+{{{
+Convert BAM to SAM:
+ samtools view -h -o foo.sam foo.bam
+}}}
+{{{
+Sort BAM file (where ".bam" is added to "foo.sorted")
+ samtools sort foo.bam foo.sorted
+}}}
+{{{
+Index a sorted BAM file (which creates foo.sorted.bam.bai):
+ samtools index foo.sorted.bam
+    
+Both foo.sorted.bam and foo.sorted.bam.bai are needed for visualization.
+ }}}  
+
+=== Count the number of mapped reads by chromosome ===
+
+{{{
+Method 1 (all chromosomes)
+1 - Index the BAM file: 
+ samtools index mapped_reads.bam
+2 - Get index statistics (including the number of mapped reads in the third column: 
+ samtools idxstats mapped_reads.bam
+}}}
+
+{{{
+Method 2 (one chromosome, without a BAM index)
+From SAM
+ awk -F"\t" '$3 == "chr2" {print $1}' mapped_reads.sam | sort -u | wc -l
+From BAM
+ samtools view mapped_reads.bam | awk -F"\t" '$3 == "chr2" {print $1}' | sort -u | wc -l
+}}}
+
+=== Remove unmapped reads ===
+
+
+{{{
+samtools view -hS -F 4 mapped_unmapped.sam > mapped_only.sam
+}}}
+
+
+=== How many multiple/uniquely mapped reads are in a bam/sam file?
+
+{{{
+bam_stat.py -i mapped_reads.bam
+}}}