Question: StringTie - Multimapped reads
1
gravatar for sneha108.ss
8 days ago by
sneha108.ss0 wrote:

Hello,

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.

Thanks

ADD COMMENTlink modified 5 days ago by kristoffer.vittingseerup1.2k • written 8 days ago by sneha108.ss0
0
gravatar for kristoffer.vittingseerup
5 days ago by
European Union
kristoffer.vittingseerup1.2k 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 5 days ago by kristoffer.vittingseerup1.2k
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