This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Why FS is low when reads aligned from strand seem biased?

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

exome variant calling vcf
• 1,575 views • link
updated by finswimmer finswimmer • written by Sharon Sharon

1 answer

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

• 0 views • link
written by finswimmer finswimmer

Got it, thanks finswimmer.

• 0 views • link
written by Sharon Sharon

Fine :)

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

fin swimmer

• 0 views • link
written by finswimmer finswimmer

Log in to answer this question.

More posts like this