Populate reference data matrix about htsinfer HOT 10 CLOSED

From the 400-something species that are in the set of ribosomal transcripts I have created clusters based on taxonomical rank "class" to obtain the most diverse subset of species and picked one from each of the 50 cluster and mined the SRA for experiments which are Single-end, Paired-end and from one interval of the specified lengths(<30,<80, <130, <180). I obtained +300 results, from which only 83 had a pubmed-id associated with them, those are the records that I appended into the HTSinfer test data table. I didn't yet go through the publications, maybe it would be nice if some other pair of eyes checks it, anyway no problem for me to search for library and adapter info in the publications, just not sure wether we need so many test datasets, or should we want more perhaps?

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Awesome job @BorisYourich!

Actually, we were planning to spend an afternoon session with 10 people or so mining, so that the work isn't so dull on any one person. Your work is absolutely perfect for that, because all we need to do is go through the publications and check for the info we need (sequencing kit, most importantly, or adapter, length, orientation directly, if available).

FYI @mzavolan

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Hey, I am sorry I didn’t collect all the samples yet, had a very hectic two weeks with onboarding on the new project, though I dedicated tommorow to this project, will run the mining scripts and share all the results.

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I think we have done this, no, @balajtimate? I will close it, please re-open if you think it's not solved.

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Alright, I am happy you like it 😃 glad to have helped, good luck with mining the publications 👍

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Looking at the list of organisms that you ended up sampling, I thought that maybe we could also have some more representation by the more common organisms and closely related species. Would it be easy for you to go through the same selection process for a given list of species?

If so, could you do this for the following?

# primates
cjacchus
hsapiens
mmulatta
pabelii
panubis
ppaniscus
ptroglodytes

# livestock
btaurus
chircus
ecaballus
ggallus
oaries
sscrofa

# rodents
cporcellus
mauratus
mmmarmota
mmusculus
ocuniculus
rnorvegicus

# fungi
pmexicana
scervisiae
spombe

# plants
athaliana
bvulgaris
cjaponica
osativa
zmays

# worms
celegans
cbriggsae

# fish
drerio
olatipes
xmaculatus

# insects
amellifera
bmori
dmelanogaster

# amphibians & reptiles
acarolinensis
xtropicalis

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Sure no problem, though I won’t manage today. Hopefully tomorrow it will be ready.

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Great. Tomorrow is totally fine. In fact, the earliest we will need it is next Friday.

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Ah, before I forget: We kinda need the SRR identifiers of the actual libraries. We can easily get them from the SRX identifiers, so no need to change that for the available ones. But if it's easy to include them for the new ones, then it would be good to include them.

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@BorisYourich: did you have a chance to look at this?

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