User: abascalfederico

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Posts by abascalfederico

<prev • 173 results • page 1 of 18 • next >
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Tool to segment genome according to SNP density?
... Can anyone recommend a tool to segment the genome according to SNP density (using HMM-based segmentation, for example)? Thanks! ...
hmm snp density segmentation written 10 weeks ago by abascalfederico980 • updated 9 weeks ago by Biostar ♦♦ 20
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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 5 months ago by abascalfederico980
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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 5 months ago by abascalfederico980 • updated 5 months ago by trausch760
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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 5 months ago by abascalfederico980
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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 5 months ago by abascalfederico980
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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 6 months ago by abascalfederico980
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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 7 months ago by abascalfederico980
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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 7 months ago by abascalfederico980
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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 7 months ago by abascalfederico980
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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 7 months ago by abascalfederico980

Latest awards to abascalfederico

Popular Question 6 weeks ago, created a question with more than 1,000 views. For strange issues with absent EOF markers in BAM files
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Duplicated read names in Fastq file
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Duplicated read names in Fastq file
Popular Question 5 months ago, created a question with more than 1,000 views. For List of CNV (copy number variation) regions in the human genome
Student 5 months ago, asked a question with at least 3 up-votes. For Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
Commentator 6 months 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 7 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 9 months ago, created a question with more than 1,000 views. For F3 test for admixture
Commentator 10 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 10 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 14 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Student 14 months ago, asked a question with at least 3 up-votes. For Samtools' mpileup with pysam: enabling and disabling BAQ probabilistic realignment
Scholar 14 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 20 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 21 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Scholar 21 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 22 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Scholar 22 months ago, created an answer that has been accepted. For A: How to properly merge multiple runs into one bam file ?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: distance between two genes
Scholar 23 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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