User: abascalfederico
abascalfederico • 1.0k
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Posts by abascalfederico
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... For a given position, I want to read the pileup and when there is a match to the variant, I want to get the mapping coordinates of the read matching the variant. I do not have the exact code yet, but it would imply something like:
for pileupcolumn in samfile.pileup(chr,int(pos)-1,int(pos)):
...
written 3 months ago by
abascalfederico • 1.0k
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... Thanks, Devon. I don't want the programmatic burden ;-) I will instead make a call to python from R - not what I wanted though ...
written 3 months ago by
abascalfederico • 1.0k
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... Thanks Devon, I already had a look at that function, but it just provide a table of counts. I need to identify which reads support a given variant. This is relatively easy with pysam but I find no way to do this in Rsamtools. Maybe I missed something from the documentation? ...
written 3 months ago by
abascalfederico • 1.0k
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... For a given position, in which there is a variant called by some algorithm, I want to get the pileup and analyse the reads supporting that variant. Any idea on how to do this in R?
I know how to do this in Python using pysam but I need an R implementation.
Thanks!
...
written 3 months ago by
abascalfederico • 1.0k
• updated
3 months ago by
Devon Ryan ♦ 79k
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... Can anyone recommend a tool to segment the genome according to SNP density (using HMM-based segmentation, for example)?
Thanks!
...
written 7 months ago by
abascalfederico • 1.0k
• updated
7 months ago by
Biostar ♦♦ 20
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... That's exactly what I needed, thanks! ...
written 10 months ago by
abascalfederico • 1.0k
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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 10 months ago by
abascalfederico • 1.0k
• updated
10 months ago by
trausch • 1.0k
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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 11 months ago by
abascalfederico • 1.0k
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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 11 months ago by
abascalfederico • 1.0k
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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 12 months ago by
abascalfederico • 1.0k
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