User: abascalfederico
abascalfederico • 930
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Posts by abascalfederico
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3
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... I know they are popular but Venn diagrams with more than 3 sets are very hard to read!! Why not just a matrix (table) with the numbers for all sets intersections, diagonals having the size of the sets? Or if you want to some graph rather than a table, why not a multidimensionality reduction strategy ...
written 25 days ago by
abascalfederico • 930
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... It seems your key is both, the location and the position. I would use a hash like `$hash{"$location:$position"} = 1`. ...
written 4 weeks ago by
abascalfederico • 930
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... 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 4 weeks ago by
abascalfederico • 930
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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 4 weeks ago by
abascalfederico • 930
0
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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 5 weeks ago by
abascalfederico • 930
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128
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... Might be worth trying bwa and comparing results. If these are paired end reads I would expect a smaller proportion of multiple mappings. ...
written 7 weeks ago by
abascalfederico • 930
1
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... 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 7 weeks ago by
abascalfederico • 930
0
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... 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 7 weeks ago by
abascalfederico • 930
1
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143
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... 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 7 weeks ago by
abascalfederico • 930
1
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0
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143
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... 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 8 weeks ago by
abascalfederico • 930
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