User: pristanna

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pristanna520
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520
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Czech Republic
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5 days, 15 hours ago
Joined:
5 years, 1 month ago
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Posts by pristanna

<prev • 14 results • page 1 of 2 • next >
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Comment: C: cDNA to protein conversion
... Good start would be to find out which transcript was used to describe the nucleotide change. Then you can choose corresponding transcript for example from [Ensembl][1] and download its sequence from the box on the left (Sequence > cDNA/Protein) and modify corresponding nucleotide). Good tools for ...
written 7 weeks ago by pristanna520
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Comment: C: How to predict the effect of DNA base deletion on protein?
... VEP and SnpEff are good if you want a command-line tool to integrate into your pipeline. If you want to further investigate the consequences of just a couple of variants, you can try for example [PredictSNP2][1], [Consurf][2], [ProtScale][3] and [Protter][4]. [1]: https://loschmidt.chemi.muni.c ...
written 7 months ago by pristanna520
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Answer: A: MinIon 2D reads
... Hi midox, each molecule of DNA is double stranded, one end contains a loading adaptor and the second one a hairpin adaptor. Firstly, one strand of DNA (called template) is passed through the pore, followed by the hairpin adaptor and then by the second strand (called complement). Then, the informati ...
written 3.1 years ago by pristanna520
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Comment: C: multiple paired-end files for one sample?
... Yes, if they are not compressed, simply cat all R1 into one file and all R2 into another one. If the files are compressed, read the link from genomax2. (Or just make sure that the sum of lines in all R1 (and R2) files is equal to the number of lines in the multiple R1 and R2 files). ...
written 3.7 years ago by pristanna520
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Answer: A: multiple paired-end files for one sample?
... If the reads within the files are NOT of the same length, and you want to do absolute length based trimming, you should trim the files separately and then join them. If the reads are of the same length, the result should be the same in both scenarios. Maybe you will find useful another thread about ...
written 3.7 years ago by pristanna520
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Answer: A: R Plot: Plotting range of negative and positive values in different color
... There is a nice post about subsetting in R: http://www.ats.ucla.edu/stat/r/faq/subset_R.htm And there is how you can do it: set=read.table("input.txt") subset1 <- subset(set, V2 > -4 & V2 <= 0) subset2 <- subset(set, V2 > 0 & V2 < 4) plot(set, col="grey", ylim=c(-10,10), ...
written 4.1 years ago by pristanna520
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Answer: A: Mitochondrial genes in autosomes in humans
... I am not sure if the hypothesis is that there are functional genes on the autosomes that were inserted from mitochondria or if these are just pseudogenes or insertions of mtDNA.  But maybe you will find these resources helpful... New article about nuclear mitochondrial insertions (numts) http://www ...
written 4.1 years ago by pristanna520
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Comment: C: Tool to obtain phased genotypes for family quartet?
... I have fastq files, bam files, vcf files - so I can start from whatever point. RTG looks promising, it should be able to analyze also the quartet. Because GATK and Beagle as far as I know could analyze just trios. So thanks a lot for your recommendation!   ...
written 4.1 years ago by pristanna520
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Comment: C: adding RG tags to sorted bam file
... I can recommend Picard:  java -jar $picard_dir/AddOrReplaceReadGroups.jar   ...
written 4.1 years ago by pristanna520
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Tool to obtain phased genotypes for family quartet?
... Dear all, could anyone recommend me a command line tool / strategy to obtain phased genotypes for family quartet from NGS data? The output should be VCFv4.1 (in order to be able to upload it to GEMINI db). Thanks a lot for your ideas!   ...
quartet ngs haplotype family phasing written 4.1 years ago by pristanna520 • updated 4.1 years ago by Len Trigg1.2k

Latest awards to pristanna

Scholar 5 months ago, created an answer that has been accepted. For A: Mitochondrial genes in autosomes in humans
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Tool to obtain phased genotypes for family quartet?
Scholar 4.0 years ago, created an answer that has been accepted. For A: Mitochondrial genes in autosomes in humans
Good Answer 4.1 years ago, created an answer that was upvoted at least 5 times. For A: How To Get Bed File Containing Exons Of Canonical Transcripts And Their Correspo
Scholar 4.1 years ago, created an answer that has been accepted. For A: Mitochondrial genes in autosomes in humans
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: How To Get Bed File Containing Exons Of Canonical Transcripts And Their Correspo
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: How To Get Bed File Containing Exons Of Canonical Transcripts And Their Correspo

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