User: YaGalbi
YaGalbi • 1.3k
- Reputation:
- 1,290
- Status:
- Trusted
- Location:
- Biocomputing, MRC Harwell Institute, Oxford, UK
- Website:
- https://github.com/roo...
- Last seen:
- an hour ago
- Joined:
- 2 years ago
- Email:
- r**********@gmail.com
Microbiology BSc Hons 2016
Bioinformatics MSc Distinction 2017
Bioinformatics Prize 2017
Posts by YaGalbi
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... Thanks Genomax.
I read the key point as "Since you are sampling from **the same library data** produced by multiple runs should have similar distribution of reads."
So lans/runs don't really matter as long as they come from the same library? For clarity, I'm defining a library as a single epindorf ...
written 29 days ago by
YaGalbi • 1.3k
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... This question: ["Can we concatenate two fastq files from same sample but different runs"][1] has me confused unfortunately.
Maybe I should know better by now , but rather than sweeping it under the carpet I'd rather clear up the confusion:
I was under the impression that any form of replicate sh ...
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... Whether a separate run or separate lane makes little difference, they are still technical replicates. They should not be merged. ...
written 4 weeks ago by
YaGalbi • 1.3k
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... Mark duplicates is doing something other than just removing duplicates, otherwise it would just be called remove duplicates. My guess is that 17M have flag 1024, and the 3M have a different flag - but what is it?
I would find a command that lets me print the 3M reads that are the difference between ...
written 4 weeks ago by
YaGalbi • 1.3k
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... "However if I run it with REMOVE_DUPLICATES=FALSE and then use samtools to remove the 1024 flagged reads I end up with 56 million reads"
" It's not that using Samtools rmdup is removing fewer reads, I have never even tried it"
How do you expect an answer if you can't give clear information in the ...
written 4 weeks ago by
YaGalbi • 1.3k
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... Yes, I've started the pipeline for the data, should have the bams tomorrow and the vcfs on friday. thank you. ...
written 5 weeks ago by
YaGalbi • 1.3k
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... exactly what i was thinking - it could be better, but it really isn't that bad. ...
written 5 weeks ago by
YaGalbi • 1.3k
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... Edited ... thank you ...
written 5 weeks ago by
YaGalbi • 1.3k
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5 follow
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... Hi all,
Please take a look at these sequence quality histograms from fastqc.
Sample 1:
![Sample 1][1]
Sample 2:![Sample 2][2]
This is WGS data sequenced on illumina HISEQ4000. We intend to call snps and indels and possibly structural variants. In the future we may even use the data set for imput ...
written 5 weeks ago by
YaGalbi • 1.3k
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... Cant up vote what mastal511 said enough. You literally have less than 1% idea of what your data is. For all you know it could be contaminated.
On a side note - If there is no reference genome, why don't you make an attempt at de-novo assembly and try to get it published? ...
written 5 weeks ago by
YaGalbi • 1.3k
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For C: Displaying genes in genome browsers
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7 weeks ago,
created an answer that has been accepted.
For C: Displaying genes in genome browsers
Scholar
7 weeks ago,
created an answer that has been accepted.
For C: Displaying genes in genome browsers
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For Rshiny - How do I check if user input exists in my data set?
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For Rshiny - How do I check if user input exists in my data set?
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For Quantile normalisation: raw rpkm or log2rpkm?
Popular Question
11 weeks ago,
created a question with more than 1,000 views.
For Rshiny - How do I check if user input exists in my data set?
Autobiographer
4 months ago,
has more than 80 characters in the information field of the user's profile.
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5 months ago,
created a question with more than 1,000 views.
For RNA-seq RPKM significance cut off
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6 months ago,
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For A: wig files to bigwig using UCSC kent
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received more than 100 upvotes.
Scholar
8 months ago,
created an answer that has been accepted.
For C: Displaying genes in genome browsers
Scholar
8 months ago,
created an answer that has been accepted.
For C: Displaying genes in genome browsers
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8 months ago,
created a question with more than 1,000 views.
For RNA-seq RPKM significance cut off
Scholar
8 months ago,
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For C: Displaying genes in genome browsers
Popular Question
12 months ago,
created a question with more than 1,000 views.
For RNA-seq RPKM significance cut off
Scholar
13 months ago,
created an answer that has been accepted.
For C: Displaying genes in genome browsers
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For Is annotation of enhancers to nearest gene pointless?
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For Better for my career: Degree in computer science or Phd in bioinformatics?
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