User: alslonik

gravatar for alslonik
alslonik50
Reputation:
50
Status:
Trusted
Location:
Israel
Last seen:
2 days, 1 hour ago
Joined:
1 year, 5 months ago
Email:
a*******@gmail.com

ARO, Voulkani research center

Posts by alslonik

<prev • 28 results • page 1 of 3 • next >
0
votes
1
answer
103
views
1
answers
Comment: C: Genome de novo annotation with Maker
... Got you. Thanks again! ...
written 5 days ago by alslonik50
0
votes
1
answer
103
views
1
answers
Comment: C: Genome de novo annotation with Maker
... Many thanks for your help, Jean, I am following your advice and excluding the protein sequences. The question is now- which protein db did you use? Only uniprot? Or combined with refseq? Isn't it redundant? Do you exclude the transposon sequences as it is pointed out in the Maker wiki? Do you do i ...
written 5 days ago by alslonik50
0
votes
4
answers
1.3k
views
4
answers
Comment: C: How to align a protein set to a genome?
... You're right. I will. ...
written 10 days ago by alslonik50
0
votes
4
answers
1.3k
views
4
answers
Comment: C: How to align a protein set to a genome?
... Here is what they say on the MUMmer4.x README: > promer is for the protein level, all-vs-all comparison of nucleotide sequences contained in multi-FastA data files. The nucleotide input files are translated in all 6 reading frames and then aligned to one another via the same methods as nucmer. ...
written 10 days ago by alslonik50
0
votes
4
answers
1.3k
views
4
answers
Comment: C: How to align a protein set to a genome?
... I tried to align proteome to a genome using promer, but it treats proteins as IUPAC code for nt and turns to N all the letters that it does not recognize... Anyway I ll try to look more into their publication, thanks. PSimScan looks a good tool too! I just need an "approximate" alignment at this sta ...
written 10 days ago by alslonik50
0
votes
4
answers
1.3k
views
4
answers
Comment: C: How to align a protein set to a genome?
... May I also ask here if Promer (MUMmer) has an option of aligning a proteome to a genome? According to what i see it uses only nucleotide sequences, am I missing smth? ...
written 10 days ago by alslonik50
1
vote
4
answers
1.3k
views
4
answers
Comment: C: How to align a protein set to a genome?
... I think you meant tblastn and not Blasx ...
written 11 days ago by alslonik50
3
votes
1
answer
103
views
1
answer
Genome de novo annotation with Maker
... Hi all, I am annotating my new plant genome now and am working with Maker and its very detailed tutorial (http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018) . I have read a few really helpful posts about Maker here as well, b ...
genome annotation snap maker written 13 days ago by alslonik50
0
votes
3
answers
3.6k
views
3
answers
Comment: C: Training Augustus for Maker
... Hi, Roxane! I am annotating my plant genome now and am working with Maker and the same detailed tutorial. My question is re: SNAP now. How do you actually know that it is enough to train and you can run your final Maker run. I have tried to run it several time and there is a difference in the numbe ...
written 16 days ago by alslonik50
0
votes
2
answers
883
views
2
answers
Comment: C: GATK HaolotypeCaller takes too much time for variant calling
... OK, it works fine for scaffolds as well. My commands were: >list=$(cat scaffolds.list) >for i in $list >nohup gatk --java-options "-Xmx50g" HaplotypeCaller -R genome.fasta -I markedDup.bam -I sorted_MarkedDup.bam -L "$i" --genotyping-mode DISCOVERY -O "$i.vcf" &> $i.log & ...
written 25 days ago by alslonik50

Latest awards to alslonik

Scholar 4 months ago, created an answer that has been accepted. For A: Falcon - Estimation of free disc space needed

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 860 users visited in the last hour