Half a year into bioinformatics and I can't find a decent glossary. Seems like those who work with bioinformatics like to confuse everyone out of the field. :(
The words "read-reads" are simply jargon, I am unable to find any definition whatsoever. All index or quantifying pursuits are completely biased towards mapping data, which hinders non-experimental experiments. No one talks about how many false annotations there are out there.
Bioinformatics tools are brutally dependent on one another, but nobody seems to try and build a "suite" of tools. You have to download and download packages here and there, just to fail to use them or to test which one fits better, because I get quickly criticized by a teacher and colleagues for not approaching the vague "standards".
For what I understand, a read can be:
- All of the fragments mapped: The sequence a machine managed to detect, with all its hardware and methodical quirks.
- The sum of small sequences that were managed to be compiled into a .fasta file, for example by programs like velvet or bowtie2.
- A section of a file that I want to interact with.
I must ask out there, shouldn't there be a different, alternative, technical name for a read? I mean, when you google it, it gets confused with the verb 'to read' and the indicative, the imperative, past participle and whatnot, all of them called 'read'.
I understand why the name is a thing, that it suits well, and perhaps I have not been doing as much bioinformatics to fully understand them, but I believe scientific knowledge should avoid these language issues if it can. Or am I criticizing something uncriticizeable?