User: david.b.rombaut

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Posts by david.b.rombaut

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Comment: C: KissDE might not work with R 4.0.2 (?) - on Ubuntu
... As I see no reasons to keep using the "old" kissplice2refgenome, there is no problems anymore. Thanks ! ...
written 3 months ago by david.b.rombaut0
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Comment: C: KissDE might not work with R 4.0.2 (?) - on Ubuntu
... Ok, it has to do with kissplice2refgenome version (sorry for the delay, biostars wouldn't allow me to respond without a 6 hours wait) Indeed, the example I gave you was generated with kissplice2refgenome 1.2.3 (from the KisSplice web page). And with this version, the separator are comas ! KissDE on ...
written 3 months ago by david.b.rombaut0
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Comment: C: KissDE doesn't work with R 4.0.2 (?)
... No, it is exactly 187 samples. But the same problem has also occured on the example on the spreadsheet (with 8 samples). The first warning : 1: In matrix(unlist(split2), nrow = 3) : data length [706] is not a divisor nor a multiple of the number of lines [3] only occured on the "big" k2r ...
written 3 months ago by david.b.rombaut0
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Comment: A: KissDE doesn't work with R 4.0.2 (?)
... Hi, The computer I usually use for this doesn't have R 4.0 anymore, so I tried to replicate this on a Windows computer with R 4.0, and... it works. Note that I tested a different k2rg file, because the Windows machine is only a weak laptop that probably won't like an almost 2 Go k2rg file. Neverth ...
written 3 months ago by david.b.rombaut0
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Comment: A: KissDE doesn't work with R 4.0.2 (?)
... Hi, with 200 samples it won't look good if I paste it here ! But I guess the part that you want is this one (not from the same file, but has been processed with the same kissplice version, and has the same problem): AS1_8,SB1_8,S1_0,ASSB1_8,AS2_0,SB2_0,S2_0,ASSB2_0,AS3_0,SB3_0,S3_0,ASSB3_0,AS4_0,SB ...
written 3 months ago by david.b.rombaut0
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Comment: A: KisSplice2RefGenome version 2.0.0 error ?
... Hi Audric, I have effectively missed something, guess I wasn't attentive enough ! Not only does it work, but it is also far quicker and the number of (standard) events has increased by a good 20% (compared to the 1.2.3 version) on one of my smallest cohort. I definitely need to check that. Thank y ...
written 3 months ago by david.b.rombaut0
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Comment: C: KissDE doesn't work with R 4.0.2 (?)
... Thank you, this is indeed what I will end up doing. ...
written 3 months ago by david.b.rombaut0
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KissDE might not work with R 4.0.2 (?) - on Ubuntu
... Hi, after my inability to launch the new version of kiss2refgenome : [this post][1], I encoutered another problem. For unrelated reasons, I needed R 4.0 (I was on 3.6). Therefore, I did the upgrade in the "dumb" way, by completely removing the previous install and ALL the packages (because I figure ...
kissplice written 3 months ago by david.b.rombaut0 • updated 3 months ago by audric.cologne40
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KisSplice2RefGenome version 2.0.0 error ?
... Hi ! After version 2.5 of KisSplice, the new version of KisSplice2RefGenome seems nice, but I can't manage to launch it. Typically, I would launch the previous version with : kissplice2refgenome \ -a /media/***/gencode.v19.annotation.gtf \ -o /media/***/event.txt \ --pairedEnd T ...
kissplice written 3 months ago by david.b.rombaut0
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Answer: A: Problem with ks_debruijn4 on large dataset in KisSplice
... Hello, it is time for the update, and the good news. The 2.5.0-beta version of KisSplice was the answer for my problem. As a reminder, our (large) dataset consist of 32 samples (paired-end), 120M reads per sample, and 1.6 To of uncompressed fastq. The specs of the computer (Dell Precision 7810) a ...
written 9 months ago by david.b.rombaut0

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