User: Nastasiia

gravatar for Nastasiia
Nastasiia 10
Reputation:
10
Status:
New User
Location:
USA/Fayetteville
Last seen:
4 months, 3 weeks ago
Joined:
10 months, 3 weeks ago
Email:
o**************@gmail.com

Posts by Nastasiia

<prev • 4 results • page 1 of 1 • next >
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maker with augusuts / utr=off
... I am running Maker with augustus as gene predictor and noticed that at err output augustus 'command' is set up not to predict UTRs like here: running augustus. --------- command ------------- Widget::augustus: ~/soft/augustus-3.2.2/bin/augustus --species=phaeod --strand=backward --UTR=off --hin ...
genome_annotation maker annotation written 6 months ago by Nastasiia 10
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Comment: C: Training Augustus quality
... Thanks. Dyatom, training on Fragilariopsis cylindrus genome. Yes I did not check redundancy, should try this ...
written 7 months ago by Nastasiia 10
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Training Augustus quality
... Hi, did anyone trained augustus? I'm actually interested in training quality which you can estimate on test gene set. My pipeline in R for choosing training set is (I use gff from genbank): 1) In gff choose all the genes for which product is defined. NO hypothetical or predicted proteins. 2)remov ...
augustus annotation genome_annotation written 7 months ago by Nastasiia 10 • updated 7 months ago by Biostar ♦♦ 20
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RAY assembler. running time/memory usage
... We have 2x7.7 Gb paired end ~100bp reads. With kmer=45 option RAY assembled it for ~2h10m on 16 core 32 Gb node. Suspecting it's too fast we checked and assembled on 64core 512 Gb node. Surprisingly it was longer, ~2h20m. Command mpirun -n 16 ~/apps/Ray-2.3.1/Ray -k 45 -amos -p ~/fw.fq ~/rev.fq -o . ...
assembly ray hpc written 10 months ago by Nastasiia 10

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