Why FS is low when reads aligned from strand seem biased?

Question

[Sharon]

Hi Everyone

I wonder why the fisher strand is low whcih means no bias given the number of reads aligned from each strand which show bias? The low coverage is because of the GC content, but why FS is low here?

                       Strand+             Strand-                  FS(FisherStrand)
Sample1 
         Ref              1                        5                            3.5
         Alt              3                       12                                                        
Sample2
         Ref              2                        6                            3.5
         Alt              4                        2  
Sample3
         Ref              2                        8                            3.5        
         Alt              1                        6

Thanks

Answer 1

[finswimmer]

The fisher strand test does not describe whether you have significant more reverse or forward reads. It checks whether the ratio between reads having the REF and those having the ALT differ significant between the two strands.

fin swimmer

[Sharon]

Got it, thanks finswimmer.

[finswimmer]

Fine :)

Please mark my answer as accepted if you find it helpful.

fin swimmer