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Fair results #4

Open LisaChabrier opened 4 years ago

LisaChabrier commented 4 years ago

Hello Nika,

Can you add the results of Fair on the repository please? Thank you!

NikaAb commented 4 years ago

Hi Lisa, I uploaded the output of IMGT in https://github.com/julibinho/cloneCluster/tree/master/data/Tools_output/IMGT_output, you can start to play with them. We are currently working on the FaIR output and I will add them asap. ◦°˚(*❛ ‿ ❛)/˚°◦

LisaChabrier commented 4 years ago

Thank you! I am currently trying to compute the consensus sequences of each cluster, but I struggle on identifying which file of results from IMGT (I1_IMGT_Fo.txt to I8_IMGT_Fo.txt) is obtained from which Real data file (P1, P3 or P4). Can you help me with that?

NikaAb commented 4 years ago

That's a good point! I have to rename the fasta files or the output files... This is how the files are related : I1 for P1, I2 for P2, ... It is normal to don't find all the sequences in the fasta file, in the corresponding output. The simplest explanation would be the IMGT's criteria for sequence analysis. If a sequence is "somehow uninteresting biologically for repertoire analysis", IMGT rejects it and you would not find it the clustering result.

LisaChabrier commented 4 years ago

Hello Nika,

Can you upload the CDR3 from IMGT in nucleotides and in amino-acids please? Sorry to bother you again!

Thank you!

NikaAb commented 4 years ago

Hello everybody, Sorry for the delay (シ )シ Here are the files: https://github.com/julibinho/cloneCluster/tree/master/data/Real/Extracted_CDR3/Extracted_by_IMGT

NikaAb commented 4 years ago

Hi! You can find the Scoper R code and all the related files here : https://github.com/julibinho/cloneCluster/tree/master/data/Tools_output/Scoper

LisaChabrier commented 4 years ago

Hello! I am looking for the CDR3 extracted by IMGT for the simulated data, that I can't find on the repository. Is it possible for you to upload them?

Thank you!

julibinho commented 4 years ago

Bonjour,

Effectivement, je trouve seulement les resultats de IMGT pour les données reel cloneCluster/data/Real/Extracted_CDR3/Extracted_by_IMGT/

Pour les donnes artificiel, ça doit etre à data/Artificial/Extracted_CDR3/Extracted_by_IMGT/

Nika, ou sont les donnees?

Merci

NikaAb commented 4 years ago

Hi! Now they are here: https://github.com/julibinho/cloneCluster/tree/master/data/Artificial/Extracted_CDR3/IMGT Enjoy!