9
votes
Accepted
How to read and interpret a gene expression quantification file?
The first column contains Ensembl gene identifiers, and the suffix is a version number that can be used to track changes to the gene annotations over time. From the Ensembl Stable IDs documentation:
...
- 5,110
4
votes
Accepted
Salmon output: transcripts quantified with zero reads support
All transcripts should always be returned in the output, whether there's evidence supporting their expression or not. This is for the sake of simple convenience, since typically one would be merging ...
- 19.8k
2
votes
how is the DNA Integrity Number (DIN) calculated in Bioanalyzer/TapeStation?
Note that DIN (DNA Integrity Number) and RIN (RNA Integrity Number) are different scores. I've had trouble in the past finding code or formulas for calculating both of these scores, which is very ...
- 15.1k
1
vote
In calculating the retention index, why do we use the character state with the lowest frequency?
The maximum number of steps (or changes) is the number of taxa with state 1 or 0, whichever is smaller. Conceptually, this is the number of character changes if each taxon evolved its state ...
- 1,149
1
vote
Accepted
Exception : [Failed to read 8 bytes from input stream! Read 0] salmon quant was invoked improperly
The issue was caused by the corrupted input .fastq files that were damaged somehow upon uploading them from the local machine. We figured it out by ...
- 2,578
1
vote
how is the DNA Integrity Number (DIN) calculated in Bioanalyzer/TapeStation?
The best I could find by looking at github.com is:
https://github.com/brianfleharty/Agilent-BioAnalyzer-RIN-R-code-for-Fly/blob/master/RNA_RIN.R
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- 2,364
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