Hi all,
Can someone help me understand the RSeQC Output from infer_experiment.py?
So this is the output:
This is PairEnd Data
Fraction of reads failed to determine: 0.0560
Fraction of reads explained by "1++,1--,2+-,2-+": 0.0192
Fraction of reads explained by "1+-,1-+,2++,2--": 0.9247
So it's stranded but is it fr-firststrand or fr-secondstrand? I do not understand the help given here:
For pair-end RNA-seq, there are two different ways to strand reads (such as Illumina ScriptSeq protocol):
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
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
Thanks for your help!