Changes between Version 31 and Version 32 of SOPs/SAMBAMqc

Timestamp:

11/19/21 09:02:38 (3 years ago)

Author:

gbell

Comment:

--

SOPs/SAMBAMqc

@@ -127 +127 @@
 Fraction of reads explained by "1+-,1-+,2++,2--": 0.0193
 Fraction of reads explained by other combinations: 0.0000
-# For gene counting: (featurecounts, use -p -s 1; htseq-count, use --stranded=yes); mapping with TopHat should have been performed with --library-type=fr-secondstrand.
+# For gene counting: (featureCounts, use -p -s 1; 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):
@@ -134 +134 @@
 Fraction of reads explained by "1+-,1-+,2++,2--": 0.9807
 Fraction of reads explained by other combinations: 0.0000
-# For gene counting: (featurecounts, use -p -s 2; htseq-count, use --stranded=reverse); mapping with TopHat should have been performed with --library-type=fr-firststrand.
+# For gene counting: (featureCounts, use -p -s 2; htseq-count, use --stranded=reverse); mapping with TopHat should have been performed with --library-type=fr-firststrand.
 
 # sample output on non-stranded PE reads (since both fractions are about the same):
@@ -141 +141 @@
 Fraction of reads explained by "1+-,1-+,2++,2--": 0.4897
 Fraction of reads explained by other combinations: 0.0000
-# For gene counting: (featurecounts, use -p -s 0; htseq-count, use --stranded=no); mapping with TopHat should have been performed with --library-type=fr-unstranded.
+# For gene counting: (featureCounts, use -p -s 0; htseq-count, use --stranded=no); mapping with TopHat should have been performed with --library-type=fr-unstranded.
 
 #sample output on stranded SE reads:
@@ -148 +148 @@
 Fraction of reads explained by "++,--": 0.9865 
 Fraction of reads explained by "+-,-+": 0.0068
-# For gene counting: (featurecounts, use -s 1; htseq-count, use --stranded=yes; mapping with TopHat should have been performed with --library-type=fr-secondstrand.
+# For gene counting: (featureCounts, use -s 1; htseq-count, use --stranded=yes; mapping with TopHat should have been performed with --library-type=fr-secondstrand.
 
 #sample output on stranded SE reads:
@@ -155 +155 @@
 Fraction of reads explained by "++,--": 0.0068
 Fraction of reads explained by "+-,-+": 0.9865
-# For gene counting: (featurecounts, use -s 2; htseq-count, use --stranded=reverse; mapping with TopHat should have been performed with --library-type=fr-firststrand.
+# For gene counting: (featureCounts, use -s 2; htseq-count, use --stranded=reverse; mapping with TopHat should have been performed with --library-type=fr-firststrand.