Questions tagged [quantification]

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Mathematics of “eXpress” paper

I am trying to follow the mathematics of the original paper of eXpress , specifically regarding equations (1) to (6) in the Methods section, in which the following explanation is given: The ...
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22 views

Does StringTie use exon length for gene abundance or complete gene length?

I'm currently using StringTie with option -A for calculating gene abundance (I'm interested in TPM). While checking the manual, I couldn't find any reference to the ...
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1answer
309 views

In calculating the retention index, why do we use the character state with the lowest frequency?

To calculate the retention index for a phylogenetic tree, we use the following formula: $$\frac{\text{maximum number of steps on tree - number of steps on the tree}} {\text{maximum number of steps on ...
6
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194 views

Salmon output: transcripts quantified with zero reads support

I quantified some samples using Salmon. According to the documentation of output format, the last column of the 'Quantification File' represents the number of reads that supported the given transcript,...
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325 views

Exception : [Failed to read 8 bytes from input stream! Read 0] salmon quant was invoked improperly

I am trying to run salmon and it keeps giving me 2 java exceptions: ...
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2answers
1k views

how is the DNA Integrity Number (DIN) calculated in Bioanalyzer/TapeStation?

For DNA/RNA quantification machines like the Bioanalyzer or TapeStation, the DNA Integrity Number (DIN) or RNA Integrity Number (RIN) numbers are quoted as a measure of the fragmentation of the ...
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717 views

How to read and interpret a gene expression quantification file?

I have a gene expression quantification file from TCGA that contains the following lines: ...