Hello
I tried the tool RSeQC infer_experiment.py on my RNAseq bacterial data. I know that my data is reverse stranded but I get the following output :
This is PairEnd Data
Fraction of reads failed to determine: 0.0693
Fraction of reads explained by "1++,1--,2+-,2-+": 0.3577
Fraction of reads explained by "1+-,1-+,2++,2--": 0.5730
With the doc of RSeQC we would have expected that we obtain like 0.99 for the "1+-,1-+,2++,2--" because it is reverse stranded, or 0.5/0.5 if it wasn't stranded. But we obtain a strange middle ground.
Do you have any idea of what is happening with the data ?
Thank you
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written
by
nonolescargot •
1 answer
map your reads to the genome of interest and visualize what the alignments look like.
What clarifies a lot of ambiguities is if you align only the data from pair 2 as single-end data.
All the reads from pair 2 should align in the sense (or antisense, depending on the library prep) direction.
Now you can visualize which do not and why.
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