Questions tagged [quantification]
The quantification tag has no usage guidance.
7
questions
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10 views
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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vote
0answers
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 ...
4
votes
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
votes
1answer
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,...
0
votes
1answer
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:
...
4
votes
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 ...
11
votes
1answer
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:
...
