Changes between Version 48 and Version 49 of SOPs/miningSAMBAM

Timestamp:

10/29/20 11:54:59 (4 years ago)

Author:

gbell

Comment:

--

SOPs/miningSAMBAM

@@ -98 +98 @@
 {{{
 # Method 2 (one chromosome at a time, for example, chr2)
-# From SAM
-awk -F"\t" '$3 == "chr2" {print $1}' mapped_reads.sam | sort -u | wc -l
-# From BAM
 samtools view mapped_reads.bam chr2 | cut -f 1 | sort -u | wc -l
 }}}
@@ -118 +115 @@
 
 {{{
-samtools view -h -f 2 mapped_unmapped.sam > mapped.properly_paired.sam
-}}}
-
+samtools view -h -f 2 mapped_unmapped.bam | samtools view -bS > mapped.properly_paired.bam
+}}}
+
+=== Extract spliced reads ===
+
+{{{
+samtools view -h All_reads.bam | awk '$0 ~ /^@/ || $6 ~ /N/' | samtools view -bS > Spliced_reads.bam
+}}}
 
 === How many multiple/uniquely mapped reads are in a bam/sam file? ===