Questions tagged [quantification]

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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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4 votes
1 answer
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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 ...
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6 votes
1 answer
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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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1 answer
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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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4 votes
2 answers
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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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11 votes
1 answer
920 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: ...
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