User: hugo.avila

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hugo.avila180
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Posts by hugo.avila

<prev • 46 results • page 1 of 5 • next >
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Answer: A: Programmatically retrieving taxon classification
... This should do the trick. I did use this [other answer][1], added a loop and a little string format. The file your_list.txt contains your list of names. Here it go: cat your_list.txt | xargs -I {} sh -c "esearch -db taxonomy -query '{}' | efetch -db taxonomy -format docsum | xtrac ...
written 5 days ago by hugo.avila180
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Comment: C: snpEff for bacteria
... Hi i'm seeing the same result "splice_region_variant", did you found an answer ? ...
written 9 weeks ago by hugo.avila180
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Answer: A: Online alignment for large fasta files
... 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 12 weeks ago by hugo.avila180
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Comment: C: Can I extract annotation file from genbank format or modify on current gff file?
... 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 12 weeks ago by hugo.avila180
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Comment: C: Blastn mismatch sensitivity for HSPs
... 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 3 months ago by hugo.avila180
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Comment: C: Blastn mismatch sensitivity for HSPs
... 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 3 months ago by hugo.avila180
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Comment: C: How to make blastp show complete gene name?
... 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 3 months ago by hugo.avila180
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Comment: C: Assembly plasmid with tandem repeats of the same insert
... 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 3 months ago by hugo.avila180
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Comment: C: Assembly plasmid with tandem repeats of the same insert
... 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 3 months ago by hugo.avila180
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Answer: A: Assembly plasmid with tandem repeats of the same insert
... 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 3 months ago by hugo.avila180

Latest awards to hugo.avila

Scholar 5 days ago, created an answer that has been accepted. For A: Hybrid Assembly From Illumina and Ion Torrent Reads
Scholar 3 months ago, created an answer that has been accepted. For A: Hybrid Assembly From Illumina and Ion Torrent Reads
Scholar 3 months ago, created an answer that has been accepted. For A: Hybrid Assembly From Illumina and Ion Torrent Reads
Teacher 3 months 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 4 months ago, voted at least 25 times.
Teacher 5 months 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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