User: abascalfederico

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Posts by abascalfederico

<prev • 172 results • page 1 of 18 • next >
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Comment: C: Program to calculate and add the NM tag to a bam file
... That's exactly what I needed, thanks! ...
written 27 days ago by abascalfederico960
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Program to calculate and add the NM tag to a bam file
... 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! ...
nm bam written 27 days ago by abascalfederico960 • updated 27 days ago by trausch650
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Comment: C: Why ExAC used bwa aln instead of mem?
... 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 abascalfederico960
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Why ExAC used bwa aln instead of mem?
... 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 ...
exac bwa written 7 weeks ago by abascalfederico960
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Comment: C: Tool To Generate Venn Diagrams for 8 data sets?
... 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 abascalfederico960
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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 12 weeks ago by abascalfederico960
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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 12 weeks ago by abascalfederico960
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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 abascalfederico960
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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 abascalfederico960
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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 3 months ago by abascalfederico960

Latest awards to abascalfederico

Popular Question 4 weeks ago, created a question with more than 1,000 views. For List of CNV (copy number variation) regions in the human genome
Student 7 weeks ago, asked a question with at least 3 up-votes. For Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: Is it good practice to convert lowewst quality genotyes to missing?
Popular Question 3 months ago, created a question with more than 1,000 views. For List of CNV (copy number variation) regions in the human genome
Popular Question 4 months ago, created a question with more than 1,000 views. For F3 test for admixture
Commentator 5 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 6 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 10 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Student 10 months ago, asked a question with at least 3 up-votes. For Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
Scholar 10 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
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Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Is it good practice to convert lowewst quality genotyes to missing?
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Scholar 17 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Scholar 17 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 18 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Scholar 18 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 18 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: distance between two genes

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