Questions tagged [quantification]

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Salmon Multiple File SCRIPT giving error

Hi I am using Salmon quantitation for multiple fastq paired files using following code ...
Malik Saad's user avatar
1 vote
0 answers

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 ...
Siddharth's user avatar
  • 345
4 votes
1 answer

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 ...
Namenlos's user avatar
  • 317
6 votes
1 answer

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,...
aechchiki's user avatar
  • 2,676
0 votes
1 answer

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: ...
Nikita Vlasenko's user avatar
4 votes
2 answers

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 ...
719016's user avatar
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11 votes
1 answer

How to read and interpret a gene expression quantification file?

I have a gene expression quantification file from TCGA that contains the following lines: ...
0x90's user avatar
  • 1,427