User: Macspider

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Macspider2.7k
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Vienna - BOKU
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Posts by Macspider

<prev • 525 results • page 1 of 53 • next >
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Extracting divergence times from 4DTv
... Hello everyone, I have just finished generating a 4DTv plot ([example][1]) for paralog and ortholog genes in a project I'm working on. While reading some papers where they also have made such a plot (listed in the introduction [here][2]), I see that many times they estimate divergence times betwee ...
substitution variants time 4dtv divergence written 5 weeks ago by Macspider2.7k
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Comment: C: How to calculate 4DTv distance (D4DTv) that stands for fourfold synonymous thir
... Do you have an answer to your question? I'm doing it now and it is not easy to find people who did it already. ...
written 9 weeks ago by Macspider2.7k
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Answer: A: SplitsTree command line mode
... I answer my own question for future readers: If you define `--input ...
written 11 weeks ago by Macspider2.7k
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SplitsTree command line mode
... Hi all, I am trying to integrate SplitsTree4 in a pipeline I'm working on. The manual explains quite clearly how to structure this: - an input file - a command file with operations I have followed these instructions and made a command file that looks like this: begin SplitsTree; S ...
phylogeny command line splitstree pipeline network written 11 weeks ago by Macspider2.7k
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Comment: C: 4/6 genotype in VCF
... @cmdcolin literally answered this question of yours. ...
written 3 months ago by Macspider2.7k
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Comment: C: 4/6 genotype in VCF
... That is true, if you allow multiple nucleotide polymorphisms. My bad, I was imprecise :) ...
written 3 months ago by Macspider2.7k
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Comment: C: what is the easiest/fastest way to convert from BAM to GTF
... As said by @EagleEye, what you just mentioned doesn't sound like something you would like to do. A Bam file contains records organized by read and mapping position, a Gtf contains features with start-end positions and correspondent parent feature (like exons in a gene). ...
written 3 months ago by Macspider2.7k
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Answer: A: how specify feature type in featureCounts
... Your feature is defined by the 3rd column of your GTF/GFF file. As you said, the default is exon, but you can change it to any of the features that you have in your GTF file. `cut -f 3 | sort | uniq` will give you all the possible features you can use. Regardless of the feature you choose, featur ...
written 3 months ago by Macspider2.7k
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Comment: C: 4/6 genotype in VCF
... Genotypes work like this: - 0: same as reference - 1: first alternate allele - ... - *n*: *n*-th alternate allele Where *n* has to be < (strictly lower than) the number of letters that compose your base space. In case of DNA, you have four (A,C,T,G), so you can expect at most 4-1=3 alterna ...
written 3 months ago by Macspider2.7k
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Comment: C: hisat2 warning message dunring alignment of fasta file with reference genome
... Perhaps the files are named differently but they contain the same reads inside and there was a mixup before alignment? ...
written 3 months ago by Macspider2.7k

Latest awards to Macspider

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 5 weeks ago, created a question with more than 1,000 views. For DESeq2 proper design setting
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: How to add tophat and bowtie to the path?
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Great Question 6 weeks ago, created a question with more than 5,000 views. For Best way to compare two samples in a VCF file
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: How to add tophat and bowtie to the path?
Scholar 3 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Good Question 6 months ago, asked a question that was upvoted at least 5 times. For Best way to compare two samples in a VCF file
Popular Question 6 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Popular Question 7 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 10 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Appreciated 11 months ago, created a post with more than 5 votes. For Best way to compare two samples in a VCF file
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 11 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 12 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 12 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 13 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 13 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 14 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Appreciated 14 months ago, created a post with more than 5 votes. For Best way to compare two samples in a VCF file
Scholar 16 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'

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