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
•
written
by
sneha108.ss •
1 answer
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
Log in to answer this question.
-
Trying to understand STAR fastqLog.final.out File
written by Daniel •
-
Bowtie2 -R parameter
written by Jonathan •
-
STAR and StringTie to identify novel isoforms (please check my work)
written by Jen •
-
RNA-seq transcript assembly, novel transcript identification and visualisation
written by andreismolnikov00 •
-
What impact does sorting by read name have on RSEM abundance estimates
written by adam.faranda
-
Map illumina reads to multi-fasta in "no mismatches" mode with statistics
written by grassostefan •
-
How does DEXSeq calculate exon usage values
written by sneha108.ss •
-
STAR output - high multi-mapping, low alignment (human)
written by anikb •
-
question about stringtie arguments
written by sophialovechan •
-
Mpileup Output And Quality Scores
written by NextGenSeek •
