User: Macspider

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Macspider2.6k
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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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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 10 hours ago by Macspider2.6k
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Answer: A: SplitsTree command line mode
... I answer my own question for future readers: If you define `--input ...
written 20 days ago by Macspider2.6k
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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 20 days ago by Macspider2.6k
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Comment: C: 4/6 genotype in VCF
... @cmdcolin literally answered this question of yours. ...
written 5 weeks ago by Macspider2.6k
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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 5 weeks ago by Macspider2.6k
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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 5 weeks ago by Macspider2.6k
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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 5 weeks ago by Macspider2.6k
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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 5 weeks ago by Macspider2.6k
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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 7 weeks ago by Macspider2.6k
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Comment: C: Problems running variant calling (VC) GATK: SAM/BAM/CRAM file dedup.bam is malfo
... Both Devon and Genomax are right, because - at least my personal experience - it depends on your analysis. Are you running an analysis composed of different replicates/accessions/genomes/species, or are the data coming from one source and one replicate? - Many sources: add read groups that make ...
written 7 weeks ago by Macspider2.6k

Latest awards to Macspider

Scholar 5 weeks ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Good Question 3 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 3 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Popular Question 5 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 8 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Appreciated 9 months ago, created a post with more than 5 votes. For Best way to compare two samples in a VCF file
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 9 months ago, created an answer that has been accepted. 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'
Scholar 10 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 10 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 11 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 12 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Appreciated 12 months ago, created a post with more than 5 votes. For Best way to compare two samples in a VCF file
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 14 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Scholar 14 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 15 months ago, created a question with more than 1,000 views. For Best way to compare two samples in a VCF file
Student 18 months ago, asked a question with at least 3 up-votes. For DESeq2 proper design setting
Scholar 18 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'

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