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User: antonioggsousa

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Posts by antonioggsousa

<prev • 26 results • page 1 of 3 • next >
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Job: Bioinformatics Post-doctoral position at Gulbenkian Institute Portugal
... Job summary: A call is open for a Postdoctoral Fellowship (BPD) for PhD holder under the R&D Unit with reference ‘Instituto Gulbenkian de Ciência UID/Multi/04555’ at the IGC - Instituto Gulbenkian de Ciência, Oeiras, Portugal, funded by national funds through FCT/MCTES (PIDDAC), as follows: ...
assembly genome job snp R rna-seq written 3 months ago by antonioggsousa • 90
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Comment: C: How do I get the unique SNPs for each strain?
... Thank you Pierre Lindenbaum! I tested and it seem to work. António ...
written 3 months ago by antonioggsousa • 90
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How do I get the unique SNPs for each strain?
... Hi, First, I would like to say that I'm new to genome and variant calling data analyses and, of course, to GATK. I read some tutorials and the BestPractices guide before I start. I'm using gatk version 4.1.4.0. So, let's go to the point. I have a couple of genomes for different yeast strains. I' ...
snp written 3 months ago by antonioggsousa • 90 • updated 3 months ago by Pierre Lindenbaum ♦ 126k
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Comment: C: How to perform local realignment around indels without a known vcf file of indel
... Thank you @Marks! I read that to, but I found at this link - https://software.broadinstitute.org/gatk/blog?id=7847 - that we should still do the local realignment, and that's why I asked. António ...
written 3 months ago by antonioggsousa • 90
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Answer: A: select() not working in R
... Hi, select() is a method to select a column based on their name, ie, column name, and you are indexing the column. So, just do: > x <- select(mt_coding_variants, REF) This is enough to select your column. António ...
written 3 months ago by antonioggsousa • 90
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Answer: A: metagenomics- read based diversity analysis
... Hi @biobiu, Yes, the [phyloseq][1] R package performs alpha- and beta-diversity metrics based on absolute read-abundance such as Shannon diversity (alpha) and Bray-Curtis dissimilarity (beta). There is also another R package that is useful to determine rarefaction curves and perform several alpha- ...
written 3 months ago by antonioggsousa • 90
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How to perform local realignment around indels without a known vcf file of indels with GATK?
... Hi, I work last few years on bioinformatics, but my knowledge is basically limited to the processing of amplicon and metagenomics NGS data. Recently, I started to work with genome assemblies and call variants but I lack the knowledge and experience. So, I have a couple of genomes from different s ...
next-gen snp written 3 months ago by antonioggsousa • 90 • updated 3 months ago by Amar • 640
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Comment: C: how to plot an abundance table with ssp from metagenominc data
... That makes sense (that the name column in your `df` is the `col.names`). The `measure` variable is missing in the `df`. Sorry! You just need to add a column with a character variable saying `Shannon` for all the observations and you can give as column name `measure`. Try that and please let me k ...
written 7 months ago by antonioggsousa • 90
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Answer: A: how to plot an abundance table with ssp from metagenominc data
... Hi @Lila M, The first thing that you shouldn't do is to add your column named "name" with the species abundance data with the `diversity()` function. Otherwise, it will include this column as species abundance data. Therefore I suggest to use the following (to remove the first column): shann ...
written 7 months ago by antonioggsousa • 90
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Comment: C: Error in correlation plot display in R
... Can you do print of the header of your table? Try: > head(pears) I think that your column names are the first row. If they are in the first row, you need to exclude them by using: > pears <- pears[-1,] This last command will exclude the first row of pears. I hope that this helps! ...
written 7 months ago by antonioggsousa • 90

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