Changes between Version 18 and Version 19 of SOPs/miningSAMBAM

Timestamp:

06/05/14 22:39:08 (11 years ago)

Author:

byuan

Comment:

--

SOPs/miningSAMBAM

@@ -116 +116 @@
 bsub "qualimap rnaseq -bam myFile.bam -gtf Homo_sapiens.GRCh37.72.canonical.gtf -outdir output_qualimap_rnaseq -protocol non-strand-specific"
 }}}
+
+
+==== infer_experiment.py from RseQC package: can be used to check if the RNA-seq reads are stranded. ====
+{{{
+
+# Command line:
+
+bsub infer_experiment.py -i accepted_hits.bam -r hs.bed
+
+-i INPUT_FILE in SAM or BAM format
+-r Reference gene model in bed fomat.
+
+# sample output on strand-specific PE reads:
+This is PairEnd Data
+Fraction of reads explained by "1++,1--,2+-,2-+": 0.0193
+Fraction of reads explained by "1+-,1-+,2++,2--": 0.9807
+Fraction of reads explained by other combinations: 0.0000
+
+# sample output on non-stranded PE reads:
+This is PairEnd Data
+Fraction of reads explained by "1++,1--,2+-,2-+": 0.5103
+Fraction of reads explained by "1+-,1-+,2++,2--": 0.4897
+Fraction of reads explained by other combinations: 0.0000
+
+For pair-end RNA-seq, there are two different ways to strand reads:
+  i) 1++,1--,2+-,2-+
+     read1 mapped to '+' strand indicates parental gene on '+' strand
+     read1 mapped to '-' strand indicates parental gene on '-' strand
+     read2 mapped to '+' strand indicates parental gene on '-' strand
+     read2 mapped to '-' strand indicates parental gene on '+' strand
+  ii) 1+-,1-+,2++,2--
+     read1 mapped to '+' strand indicates parental gene on '-' strand
+     read1 mapped to '-' strand indicates parental gene on '+' strand
+     read2 mapped to '+' strand indicates parental gene on '+' strand
+     read2 mapped to '-' strand indicates parental gene on '-' strand
+
+For single-end RNA-seq, there are two different ways to strand reads:
+  i) ++,--
+     read mapped to '+' strand indicates parental gene on '+' strand
+     read mapped to '-' strand indicates parental gene on '-' strand
+  ii) +-,-+
+     read mapped to '+' strand indicates parental gene on '-' strand
+     read mapped to '-' strand indicates parental gene on '+' strand
+
+
+}}}