User: Macspider
Macspider • 2.6k
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Posts by Macspider
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... 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
Macspider • 2.6k
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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
Macspider • 2.6k
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... 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 ...
written 20 days ago by
Macspider • 2.6k
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114
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Comment:
C: 4/6 genotype in VCF
... @cmdcolin literally answered this question of yours. ...
written 5 weeks ago by
Macspider • 2.6k
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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
Macspider • 2.6k
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... 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
Macspider • 2.6k
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... 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
Macspider • 2.6k
1
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1
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114
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1
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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
Macspider • 2.6k
0
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254
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... 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
Macspider • 2.6k
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... 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
Macspider • 2.6k
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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For Remove duplicates from reads: best practices?
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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For A: tophat --max-multihits impacts 'mapped in a proper pair'
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