Moderator: andrew.j.skelton73

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Posts by andrew.j.skelton73

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Comment: C: cross platform microarray normalization
... Hi, @ghataksoumyakanti - This thread is nearly 4 years old. Please open a new question with lots of detail to ensure that users can help you out! - [See here for how to ask a good question][1] [1]: https://www.biostars.org/p/75548/ ...
written 1 day ago by andrew.j.skelton735.8k
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Comment: C: Vcf produced after ApplyVSQR step
... Can you clarify if this is WES / WGS / Targeted sequencing? ...
written 3 months ago by andrew.j.skelton735.8k
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Answer: A: Vcf produced after ApplyVSQR step
... I'd check out [this post][1] which tries to explain VQSR all in one. Particularly look at the *How ApplyRecalibration works in a nutshell* section: > During the first part of the recalibration process, variants in your > callset were given a score called VQSLOD. At the same time, variants &g ...
written 3 months ago by andrew.j.skelton735.8k
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Comment: C: Vcf produced after ApplyVSQR step
... I've formatted your post so that your code blocks are more readable ...
written 3 months ago by andrew.j.skelton735.8k
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Comment: C: Investigating differentially expressed genes
... Do you have the loci of each SNP in a file? Also reference genome builds may play a role here - are they different between the RNAseq and GWAS platform? ...
written 3 months ago by andrew.j.skelton735.8k
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Answer: A: Kolmogorov-Smirnov Test and Shapiro-Wilk Test statistics in Proteomics
... This seems like you want to understand why these "geeky" mathematical principles are relevant to statistical modelling of biological data. This is beyond proteomics, but more orientated to fundamental assumptions of modelling. I'd recommend reading Wolfgang Huber & Susan Holmes' book, Modern Sta ...
written 3 months ago by andrew.j.skelton735.8k
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Answer: A: How to obtain multiple sequence alignments of genomes of selected vertebrate spe
... Have you considered trying out Ensembl for this problem? Buffalo (or Bison), are available in the [MSA functionalities in Ensembl][1]. Here's a [video][2] on how to perform MSA of specific species using Ensembl tools. [1]: https://www.ensembl.org/info/genome/compara/multiple_genome_alignments.ht ...
written 3 months ago by andrew.j.skelton735.8k
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Answer: A: Deal with the time-course RNA-Seq datasets
... If all you're interested in (or have to work with), is the differences between time points, then that's all you can test in your experiment. [Section 9.6.1 of the Limma users guide][1] is a good basis to start from. These principles can be applied to DESeq2 too. There are other ways to look at your ...
written 3 months ago by andrew.j.skelton735.8k
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Answer: A: Analysis of exome samples build from different exome kits
... My first inclination would be to make sure that all recommended preprocessing steps are performed with the respective kits from alignment up to gVCF generation. Once you genotype the gVCF files, try out the union or intersect of all kits (be careful with the intersect as some very old kits did not t ...
written 3 months ago by andrew.j.skelton735.8k
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Comment: C: Comparing different transcripts expression level of a list of genes from one con
... DEXseq is most likely what you want. For a single gene, you can look at the sample-wise usage metrics, such as [this visualisation][1] (third figure down). They've analysed this with a control and knockout, but you can easily just provide an intercept of 1 design (`~1`) where required. [1]: ht ...
written 4 months ago by andrew.j.skelton735.8k

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