User: abascalfederico

gravatar for abascalfederico
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Spain
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Posts by abascalfederico

<prev • 167 results • page 1 of 17 • next >
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Comment: C: Compare pairs of key/value of perl hash tables
... It seems your key is both, the location and the position. I would use a hash like `$hash{"$location:$position"} = 1`. ...
written 8 hours ago by abascalfederico890
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Comment: C: What is the most popular programming language used in bioinformatics?
... Python is very popular nowadays (I still do Perl though). Knowing some unix tools is also of great help, including commands like cut, sort, uniq, join, tr and some programming in awk + sed. And of course the R environment/languate for statistics, plotting, scripting... ...
written 8 hours ago by abascalfederico890
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Comment: C: PCA using plink files
... I'd try to add "." to the PATH, or just the full path to "lines" ...
written 15 hours ago by abascalfederico890
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Comment: C: PCA using plink files
... The error message is clear :-) It seems you have to install (or add to your path) a program called "lines" An alternative to shellfish is [smartpca][1] [1]: https://github.com/chrchang/eigensoft/blob/master/POPGEN/README ...
written 4 days ago by abascalfederico890
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Comment: C: Extracting the best reads that align multiple times
... Might be worth trying bwa and comparing results. If these are paired end reads I would expect a smaller proportion of multiple mappings. ...
written 20 days ago by abascalfederico890
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Comment: C: how can i count the total exon in the sequence structure?
... Try searching for "extracting CDS sequences from GTF" or something like. It must have been asked here A quick search found https://www.biostars.org/p/46281/ but must be others ...
written 20 days ago by abascalfederico890
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Comment: C: Problems merging the NGS data of different sequencing platform(Illumina Hiseq200
... I would expect that increasing the coverage (and the quality of calls) would reduce platform biases. With 5x you should be able to test this by analysing only those calls with high quality in both platforms. There must be good calls enough. You may want to restrict your analysis to homozygotes, whic ...
written 21 days ago by abascalfederico890
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Comment: C: how can i count the total exon in the sequence structure?
... Do you have the gene structure information also (exons, introns...)? If you have a GTF with all this information you can write a script to extract the sequence corresponding to each exon and translate according to the correct reading frame. If you are working with Nematostella, it is available in ...
written 22 days ago by abascalfederico890
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Comment: C: how can i count the total exon in the sequence structure?
... Which species are you working with? You may or may not have gene structure information for your species of interest. If not, you may use a closely related species and assume a similar gene structure. In ensembl (not only vertebrates-ensembl but metazoa-ensembl, plant-ensembl...) there are lots of sp ...
written 23 days ago by abascalfederico890
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Comment: C: Parameter to consider a hit as a gene copy
... You can use blast e-values to discern homology. If there is homology, there was a gene duplication (or domain shuffling) at some point. However, I am not sure you want to remove ALL duplicated genes, may be only those which duplicated after some point in history (e.g. divergence of rice from another ...
written 23 days ago by abascalfederico890

Latest awards to abascalfederico

Popular Question 3 days ago, created a question with more than 1,000 views. For List of CNV (copy number variation) regions in the human genome
Popular Question 8 weeks ago, created a question with more than 1,000 views. For F3 test for admixture
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Is it good practice to convert lowewst quality genotyes to missing?
Scholar 3 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 7 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Student 7 months ago, asked a question with at least 3 up-votes. For Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
Scholar 7 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Centurion 11 months ago, created 100 posts.
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Is it good practice to convert lowewst quality genotyes to missing?
Supporter 14 months ago, voted at least 25 times.
Scholar 14 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Scholar 14 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 15 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Scholar 15 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 16 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: distance between two genes

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