Question: StringTie - Multimapped reads
gravatar for
9 months ago by
sneha108.ss0 wrote:


I am using StringTie to assemble and quantify RNA seq reads. Could someone please help me understand how StringTie deals with multi-mapped reads? The manual states that the -M option "specifies the maximum fraction of multiple-location-mapped reads that are allowed to be present at a given locus" and that the default value is 0.95. I did not completely understand what this means.

Also, it will be really helpful if someone could explain how StringTie performs multi-mapping correction.

I am using StringTie version 1.3.4.


ADD COMMENTlink modified 9 months ago by kristoffer.vittingseerup2.4k • written 9 months ago by sneha108.ss0
gravatar for kristoffer.vittingseerup
9 months ago by
European Union
kristoffer.vittingseerup2.4k wrote:

From the methods section of the StringTie paper:

if a fragment aligns in n places, than that fragment alignment will contribute 1/n to the edge capacity

ADD COMMENTlink written 9 months ago by kristoffer.vittingseerup2.4k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1476 users visited in the last hour