User: Darya Vanichkina

Reputation:
100
Status:
Trusted
Location:
Australia/Centenary Institute University of Sydney
Website:
http://daryavanichkina...
Twitter:
dvanichkina
Last seen:
1 year, 8 months ago
Joined:
5 years, 3 months ago
Email:
d***********@gmail.com

Posts by Darya Vanichkina

<prev • 25 results • page 1 of 3 • next >
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Comment: C: How to normalize chromatin and RNA-Seq data together ?
... Hi! It's not clear to my what you're doing. When you say: "14 independent samples subjected <...> at different times" are you implying that:   1. The ATAC-Seq was generated at biological days 1 .. 2 .. 10 (for example) while RNA-seq was at biological days 1 ... 3 .. 5 ? 2. You sent off 14 ...
written 20 months ago by Darya Vanichkina100
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Answer: A: Comparing two RNAseq experiments using summarizeOverlaps
... The rseqc tool has a very useful tool called infer_experiment.py which you can run on your bam file (you'll need a reference annotation) to see which stranding protocol your data looks like it came from. This is very useful post-hoc even when you know the protocol of how your library was generated t ...
written 20 months ago by Darya Vanichkina100
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Comment: C: Error with featureCounts
... Also having the same problem, and not able to fix it with -p -P ... ...
written 23 months ago by Darya Vanichkina100
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Comment: C: Removing trended biases between HiC libraries
... Thanks! I was just confused why the trended M-value was being compared between two non-replicate samples.  ...
written 24 months ago by Darya Vanichkina100
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Comment: C: Interpreting strand orientation plots in diffHic
... Thanks!  OK, I've set the cutoff for outward pairs higher.  The three replicates are paired, in that Sample1"left" and Sample2"left' were generated at the same time, as were Sample1 and 2 "middle", and Sample 1 -2 "right". So that's why I think there could be some "wet-lab" variability (i.e. minor ...
written 24 months ago by Darya Vanichkina100
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Removing trended biases between HiC libraries
... In section  5.2 of the diffHic manual (Removing trended biases between libraries), why is the MA plot plotted for two non-replicate samples in the input data? ​input <- c("merged_flox_1.h5", "merged_flox_2.h5", "merged_ko_1.h5", "merged_ko_2.h5") data <- squareCounts(input, width=1e6, param= ...
diffhic written 24 months ago by Darya Vanichkina100 • updated 24 months ago by Aaron Lun21k
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Interpreting strand orientation plots in diffHic
... Hi! I've got two sets of replicate (x3) HiC libraries. I think I've set the min.inward,  min.outward and max.frag thresholds for them correctly (or at least for the bulk of the datasets - not sure if I should set the threshold for replicate 3 individually?). My question is: what is going on with th ...
diffhic written 24 months ago by Darya Vanichkina100 • updated 24 months ago by Aaron Lun21k
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goseq pwf length bias plot: interpreting plot
... Following on the question here, but with a similar and yet slightly different problem: I am also using goseq with a manually compiled annotation, and am getting a strange plot similar to the one described by the author above (but I'm not prefiltering more than I should be, *I think*): What does ...
goseq written 2.4 years ago by Darya Vanichkina100 • updated 2.4 years ago by Gordon Smyth35k
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Comment: C: biomaRt File './ensembl_mart_84/mmusculus_gene_ensembl__translation__main.MYD' n
... ensembl=useMart(host="www.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl")   ...
written 2.5 years ago by Darya Vanichkina100
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Comment: C: Gene ontology and pathway analysis in R - replicate ToppGene features; best stra
... Hi Kevin, I realised as I wrote my question, I think, that my main problem was how do I build a really awesome database of everything that I want to test for (and that ToppGene tests for me) in R... The challenge with DAVID is that, I believe, the annotations are quite old and not routinely update ...
written 2.5 years ago by Darya Vanichkina100

Latest awards to Darya Vanichkina

Popular Question 2.7 years ago, created a question with more than 1,000 views. For Yet another DESeq2 nested design contrast matrix question
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Too many (?) differentially expressed genes - edgeR and DESeq
Popular Question 2.7 years ago, created a question with more than 1,000 views. For DESeq2: add annotations (from data frame) to DESeqDataSet
Scholar 2.8 years ago, created an answer that has been accepted. For A: featureCounts (sourceforge) not returning any counts in count table, even though

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