User: VY

gravatar for VY
VY120
Reputation:
120
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London
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3 months, 2 weeks ago
Joined:
3 years, 10 months ago
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k*******@kcl.ac.uk

Posts by VY

<prev • 52 results • page 1 of 6 • next >
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Comment: C: error message when running Deseq2 on featureCounts output files
... You're probably using a dodgy GTF file that has duplicates for whatever reason. Import a GTF file. Get data > UCSC main > select your model organism and under table select "refFlat". Try re-running FeatureCounts with that. ...
written 3 months ago by VY120
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ChIPseq vs RNAseq comparison
... Hello, I have a number of RNAseq bigwigs and ChIPseq bigwigs and would like to compare overall how counts in one location compare to counts in the same location in the contrasting experiment. To plot literally something like the figure here : https://www.nature.com/articles/nn.4532/figures/14 Doe ...
chip-seq rna-seq written 3 months ago by VY120 • updated 3 months ago by Bjoern Gruening5.1k
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Comment: C: Cufflinks Failure Error
... Hi Jen, I was unable to reproduce it either. I rerun cufflinks on the same files with the same parameters a second time and it went through fine so must have been a temporary glitch somewhere. Sorry. ...
written 4 months ago by VY120
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Comment: C: Cufflinks Failure Error
... Hi Jen, Thanks for your help. I've created new jobs with the updated cufflinks - some went through and finished alright but others crashed and gave this error, do you think it's another bug? thanks! Val File "/jetstream/scratch0/main/jobs/19888009/tool_files/cufflinks_wrapper.py", line 169 ...
written 4 months ago by VY120
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Cufflinks Failure Error - Solution: use version 2.2.1.2 or later
... Hello, I've been trying to run cufflinks on my bam files for the last couple of house and keep getting the following tool error. Does anyone know if this is something to do with the bam files or is it an issue with galaxy? (Bam files were generated on the terminal using HISAT2 - not on galaxy). T ...
cufflinks rna-seq written 4 months ago by VY120 • updated 4 months ago by Jennifer Hillman Jackson25k
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Comment: C: Galaxy main glitch?
... Thanks will do that! Best wishes, Val ...
written 18 months ago by VY120
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Galaxy main glitch?
... Hi Everyone, Has anyone been having issues on galaxy (main) the last few days? I know it went down completely a couple of days ago and saw Mo's post on a different thread that is back up and running and working through the backlog, but I've been having issues the past 2 days. Jobs will either run 1 ...
maintenance galaxy main written 18 months ago by VY120 • updated 18 months ago by Martin Čech ♦♦ 4.9k
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Change Tracking Id to Gene name
... Hello, I'm not sure if this is something that can be done in galaxy, but if anyone knows how to do it in R that would help aswell. I've run cuffdiff on my samples and I've selected the output count file function. When I look at my cuffdiff gene count tracking file, all the rows are under the trac ...
cuffdiff rnaseq rna-seq written 21 months ago by VY120 • updated 21 months ago by Jennifer Hillman Jackson25k
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Comment: C: ChIP-seq sequence data sources
... Hello, again, to my knowledge, ChIPseq will not predict nucleosome spreading. Off the top of my head the only way you could INFER that from ChIPseq is if you have ChIP data done on Polycomb and/or Trithorax proteins that are known to compact or relax chromatin (e.g Ring1B and MLL1 respectively -plea ...
written 2.0 years ago by VY120
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Answer: A: chip seq data
... If you're looking at nucleosome positioning you probably need ATAC-seq data and/or DNAse -seq data etc. ChIP-seq won't give you that unless you are looking at a specific nucleosome remodeling protein (or any protein for that matter). Also specifying from what bovine tissue you want would be most hel ...
written 2.0 years ago by VY120

Latest awards to VY

Popular Question 18 months ago, created a question with more than 1,000 views. For Find Common Peaks between two independent samples
Popular Question 18 months ago, created a question with more than 1,000 views. For htseq-count issues with Deseq2
Popular Question 18 months ago, created a question with more than 1,000 views. For Metadata galaxy error
Popular Question 18 months ago, created a question with more than 1,000 views. For Mouse mm10 genome
Popular Question 18 months ago, created a question with more than 1,000 views. For Peak Calling on BED files
Popular Question 18 months ago, created a question with more than 1,000 views. For Stranded vs unstranded cufflinks
Scholar 2.0 years ago, created an answer that has been accepted. For A: chip seq data

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