Changes between Version 5 and Version 6 of SOPs/SAMBAMqc

Timestamp:

05/31/16 15:48:56 (9 years ago)

Author:

gbell

Comment:

--

SOPs/SAMBAMqc

@@ -101 +101 @@
 bam_stat.py -i myFile.bam
 }}}
-==== infer_experiment.py from RseQC package: can be used to check if the RNA-seq reads are stranded. ====
+==== infer_experiment.py from RseQC package: Check if/how your RNA-seq reads are stranded. ====
 {{{
 
@@ -109 +109 @@
 
 -i INPUT_FILE in SAM or BAM format
--r Reference gene model in bed fomat.
+-r Reference gene models in bed format (converted from GTF file).
 
-# sample output on strand-specific PE reads:
+--library-type=fr-unstranded
+--library-type=fr-firststrand
+--library-type=fr-secondstrand
+
+# sample output on strand-specific PE reads (since the first fraction is much larger than the second fraction):
+This is PairEnd Data
+Fraction of reads explained by "1++,1--,2+-,2-+": 0.9807
+Fraction of reads explained by "1+-,1-+,2++,2--": 0.0193
+Fraction of reads explained by other combinations: 0.0000
+# For gene counting with htseq-count, use --stranded=yes; mapping with TopHat should have been performed with --library-type=fr-secondstrand.
+
+# sample output on strand-specific PE reads (since the second fraction is much larger than the first fraction):
 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
+# For gene counting with htseq-count, use --stranded=reverse; mapping with TopHat should have been performed with --library-type=fr-firststrand.
 
-# sample output on non-stranded PE reads:
+# sample output on non-stranded PE reads (since both fractions are about the same):
 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 gene counting with htseq-count, use --stranded=no; mapping with TopHat should have been performed with --library-type=fr-unstranded.
 
 For pair-end RNA-seq, there are two different ways to strand reads: