Changes between Version 25 and Version 26 of SOPs/SAMBAMqc


Ignore:
Timestamp:
02/27/18 09:43:25 (7 years ago)
Author:
gbell
Comment:

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  • SOPs/SAMBAMqc

    v25 v26  
    123123Fraction of reads explained by "1+-,1-+,2++,2--": 0.0193
    124124Fraction of reads explained by other combinations: 0.0000
    125 # For gene counting with htseq-count, use --stranded=yes; mapping with TopHat should have been performed with --library-type=fr-secondstrand.
     125# 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.
    126126
    127127# sample output on strand-specific PE reads (since the second fraction is much larger than the first fraction):
    … …  
    130130Fraction of reads explained by "1+-,1-+,2++,2--": 0.9807
    131131Fraction of reads explained by other combinations: 0.0000
    132 # For gene counting with htseq-count, use --stranded=reverse; mapping with TopHat should have been performed with --library-type=fr-firststrand.
     132# 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.
    133133
    134134# sample output on non-stranded PE reads (since both fractions are about the same):
    … …  
    137137Fraction of reads explained by "1+-,1-+,2++,2--": 0.4897
    138138Fraction of reads explained by other combinations: 0.0000
    139 # For gene counting with htseq-count, use --stranded=no; mapping with TopHat should have been performed with --library-type=fr-unstranded.
     139# 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.
    140140
    141141#sample output on stranded SE reads:
    … …  
    144144Fraction of reads explained by "++,--": 0.9865
    145145Fraction of reads explained by "+-,-+": 0.0068
    146 # For gene counting with htseq-count, use --stranded=yes; mapping with TopHat should have been performed with --library-type=fr-secondstrand.
     146# For gene counting: (featurecounts, use -s 1; htseq-count, use --stranded=yes; mapping with TopHat should have been performed with --library-type=fr-secondstrand.
    147147
    148148#sample output on stranded SE reads:
    … …  
    151151Fraction of reads explained by "++,--": 0.0068
    152152Fraction of reads explained by "+-,-+": 0.9865
    153 # For gene counting with htseq-count, use --stranded=reverse; mapping with TopHat should have been performed with --library-type=fr-firststrand.
    154 
    155 
    156 For pair-end RNA-seq, there are two different ways to strand reads:
     153# For gene counting: (featurecounts, use -s 2; htseq-count, use --stranded=reverse; mapping with TopHat should have been performed with --library-type=fr-firststrand.
     154
     155
     156For paired-end RNA-seq, there are two different ways to strand reads:
    157157  i) 1++,1--,2+-,2-+
    158158     read1 mapped to '+' strand indicates parental gene on '+' strand