User: abascalfederico
abascalfederico • 960
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Posts by abascalfederico
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... That's exactly what I needed, thanks! ...
written 27 days ago by
abascalfederico • 960
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... Does anybody know of a program to add the NM tag (number of mismatches) to a BAM file?
Usually aligned BAM files come with that tag, but I've found one without it and need that information.
Thanks! ...
written 27 days ago by
abascalfederico • 960
• updated
27 days ago by
trausch • 650
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... I'll send them an email, thanks for the suggestion.
Regarding the use of bwa aln, I found it in the supplementary material of:
Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., ... & Tukiainen, T. (2016). Analysis of protein-coding genetic variation in 60,706 hu ...
written 7 weeks ago by
abascalfederico • 960
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... Anyone knows why in ExAC they used bwa `aln` instead of `mem`? I am not sure of the read lengths but somewhere said something about 150 bps x 2. Does it make sense to use bwa aln here? I though for long reads mem was the best choice
The actual parameters used in ExAC were:
bwa aln q 5 -l 32 -k ...
written 7 weeks ago by
abascalfederico • 960
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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 11 weeks ago by
abascalfederico • 960
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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 12 weeks ago by
abascalfederico • 960
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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 12 weeks ago by
abascalfederico • 960
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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 12 weeks ago by
abascalfederico • 960
0
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215
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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 3 months ago by
abascalfederico • 960
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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 3 months ago by
abascalfederico • 960
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