User: hugo.avila
hugo.avila • 160
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Posts by hugo.avila
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... Hi, try [CSAR web][1]. Just upload a reference and you 4000 genomic sequences and you will get an mummer alignment, a fast scaffold and a dot plot. But i really recommend that you perform this type of analyses locally in order to get more control of your work.
[1]: http://lu168.cs.nthu.edu.tw/C ...
written 4 days ago by
hugo.avila • 160
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... Hi, try to annotate your genome (edited fasta file) with [prokka][1]. I know that it must more easy to just correct the coordinates in the genbank file with some text edit tool, but i really dont trust that the change will work well. Prokka is very easy to use and can annotate a genome in under 20 m ...
written 4 days ago by
hugo.avila • 160
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... I don't know how to explain exactly why, because there is some difficult programming that I don't fully understand. But the reason I read about why blast is not the best tool for calling the SNP is because of its scoring functions and alignment methods. They are optimized to provide the best possibl ...
written 20 days ago by
hugo.avila • 160
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... Hi i know that i'm not answering what you asked but a few months ago i did read about snp detection algorithms and i learn that Blastn is a very error prone tool to detect small mutations like snps and smal in/dels. I strongly recommend [Dnadiff][1] from the Mummer Tools to do snap calls in large se ...
written 20 days ago by
hugo.avila • 160
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... It must exist a way to do this in the blast parameters, but i find it more easy to just `translate` the spaces to underlines (or other removable character like %):
cat original_headers.fasta | tr " " "_" > converted_headers.fasta ...
written 4 weeks ago by
hugo.avila • 160
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... hummm [it seems like although flye is better to find plasmids in a full genome assemblie it did not do well when the datasets is made only of plasmid reads.][1] Let's try to do some variant call, i think this will do. Did you make a reference like i said before (plas+repeats+mids) ? If you did:
Map ...
written 4 weeks ago by
hugo.avila • 160
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... Your welcome ! :)
> Then aligning reads with mummer
I do not recommend that you map reads with mummer it is better suited for large assembled sequences like contigs and chromosomes, i never tried to use it for long reads. If you want to map reads, you don't need to do assembly just map the re ...
written 4 weeks ago by
hugo.avila • 160
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... For the assemblie use, [Flye][1] it seems like is the [best tool for plasmids][2]:
flye --nano-raw your_long_reads.fastq --out-dir out_nano.fasta --threads 4
Your can corrected the `--threads` parameter to match your computer resources.
As for the counting of the tandem repeats because you ha ...
written 4 weeks ago by
hugo.avila • 160
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Comment:
C: mauve for contigs
... Well, if you only want the chromosome, you must map the contigs in your reference and extract those that map to it. You will probably map only the largest contig. If you map more than the largest contig, you will have to build a chromosomal scaffold, as you have so few contigs and good qualities thi ...
written 4 weeks ago by
hugo.avila • 160
0
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Comment:
C: mauve for contigs
... You do not need separated files just pass your contig file to quast. You do not need a reference as well but is cool to use one:
./quast.py -r referece.fasta your_contigs.fasta
If you have problems running quast, you can use it [through the browser.][1]
[1]: http://cab.cc.spbu.ru/quast/ ...
written 4 weeks ago by
hugo.avila • 160
Latest awards to hugo.avila
Scholar
4 weeks ago,
created an answer that has been accepted.
For A: Hybrid Assembly From Illumina and Ion Torrent Reads
Scholar
5 weeks ago,
created an answer that has been accepted.
For A: Hybrid Assembly From Illumina and Ion Torrent Reads
Teacher
5 weeks ago,
created an answer with at least 3 up-votes.
For A: How can I get 100 percent identity and coverage when I run blastp?
Supporter
5 weeks ago,
voted at least 25 times.
Teacher
10 weeks ago,
created an answer with at least 3 up-votes.
For A: How can I get 100 percent identity and coverage when I run blastp?
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