User: sneha108.ss

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Posts by sneha108.ss

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aligned.sorted.bam.edgeCount output in rMATS
... Hi, I am using rMATS to find differential splicing events. I was able to run it successfully but I'm having trouble understanding one particular output file. Could someone please let me know what the columns in the aligned.sorted.bam.edgeCount file refers to? Are the values in the second column the ...
rna-seq written 5 months ago by sneha108.ss0
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How does DEXSeq calculate exon usage values
... Hi, I am using DEXSeq to identify differential splicing events from RNA-seq data and I did not completely understand how DEXSeq calculates exon usage. It will be really helpful if someone could please explain how DEXSeq calculates exon usage values and how it differs from normalized counts. Also w ...
dexseq splicing exon usage rna-seq written 9 months ago by sneha108.ss0 • updated 9 months ago by Nicolas Rosewick8.3k
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StringTie - Multimapped reads
... 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 ...
assembly stringtie rna-seq multi-mapped reads written 9 months ago by sneha108.ss0 • updated 9 months ago by kristoffer.vittingseerup2.4k

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