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Old 02-25-2014, 03:46 AM   #3
uqfgaiti
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Location: Australia, Brisbane

Join Date: Nov 2012
Posts: 13
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Hi Blanco,

to be sure I did a quick test using infer_experiment.py,it is indeed forward-reverse. I also did a blat to the genome and I got the same result.

Quote:
This is PairEnd Data
Fraction of reads explained by "1++,1--,2+-,2-+": 0.9189
Fraction of reads explained by "1+-,1-+,2++,2--": 0.0811
Fraction of reads explained by other combinations: 0.0000

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
Based on this I ran TOPHAT with fr-secondstrand and htseq-count with -s yes
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