Questions tagged [quantification]
The quantification tag has no usage guidance.
6
questions
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0
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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 ...
- 325
4
votes
1
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692
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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 ...
- 297
6
votes
1
answer
271
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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,...
- 2,646
0
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1
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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:
...
- 2,498
4
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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 ...
- 2,234
11
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1
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920
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How to read and interpret a gene expression quantification file?
I have a gene expression quantification file from TCGA that contains the following lines:
...
- 1,387