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User: YaGalbi

gravatar for YaGalbi
YaGalbi • 1.5k
Reputation:
1,480
Status:
Trusted
Location:
Biocomputing, MRC Harwell Institute, Oxford, UK
Website:
https://github.com/roo...
Last seen:
4 months, 1 week ago
Joined:
3 years, 7 months ago
Email:
r**********@gmail.com

Microbiology BSc Hons 2016

Bioinformatics MSc Distinction 2017

Bioinformatics Prize 2017

Posts by YaGalbi

<prev • 374 results • page 1 of 38 • next >
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Comment: C: Can i use ucsc track browser without a reference organism?
... If you simply want to make a pretty picture of the comparison, then try [IBS Illistrator][1] Also see [this list of alignment visualisation software][2] [1]: http://ibs.biocuckoo.org/ [2]: https://en.wikipedia.org/wiki/List_of_alignment_visualization_software ...
written 17 months ago by YaGalbi • 1.5k
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Comment: A: What crosses to make to breed a homozygous individual?
... This looks like a high school homework or undergraduate home study question. What work have you done? What have you found out by yourself. Where are you getting confused? ...
written 17 months ago by YaGalbi • 1.5k
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Comment: C: Can i use ucsc track browser without a reference organism?
... Here are 2 MSA visualisation tools: [MSAViewer][1] and [Wasabi][2] Here are 2 R packages doing a little more: [MSA (Bioconductor)][3] and [Balcony (Cran)][4] But could we get some detail on what "features" you are trying to view/compare? [1]: http://msa.biojs.net/ [2]: http://wasabiapp.org/ ...
written 17 months ago by YaGalbi • 1.5k
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Comment: C: Confused about merging RNA-seq lanes/runs
... 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 20 months ago by YaGalbi • 1.5k
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Confused about merging RNA-seq lanes/runs
... 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 ...
lanes merge samples runs rna-seq written 20 months ago by YaGalbi • 1.5k • updated 20 months ago by genomax ♦ 78k
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Comment: C: Can we concatenate two fastq files from same sample but different runs
... Whether a separate run or separate lane makes little difference, they are still technical replicates. They should not be merged. ...
written 20 months ago by YaGalbi • 1.5k
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Answer: C: Picard MarkDuplicates flag vs remove issue
... 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 20 months ago by YaGalbi • 1.5k
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Comment: C: Picard MarkDuplicates flag vs remove issue
... "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 20 months ago by YaGalbi • 1.5k
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Comment: C: Is the sequence quality good enough?
... Yes, I've started the pipeline for the data, should have the bams tomorrow and the vcfs on friday. thank you. ...
written 20 months ago by YaGalbi • 1.5k
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Comment: C: Is the sequence quality good enough?
... exactly what i was thinking - it could be better, but it really isn't that bad. ...
written 20 months ago by YaGalbi • 1.5k

Latest awards to YaGalbi

Appreciated 17 months ago, created a post with more than 5 votes. For Update: CRISPR off-target effects causing unexpected mutations - good science or media hype?
Popular Question 17 months ago, created a question with more than 1,000 views. For Meme: What is the optimal sequence length?
Popular Question 17 months ago, created a question with more than 1,000 views. For CummeRbund: I can't create a dispersion plot - help please?
Popular Question 17 months ago, created a question with more than 1,000 views. For Rshiny - How do I check if user input exists in my data set?
Popular Question 17 months ago, created a question with more than 1,000 views. For Can anyone suggest a RShiny app for displaying RNA-seq results online
Popular Question 17 months ago, created a question with more than 1,000 views. For Nucleoatac - extending broadPeak regions
Popular Question 17 months ago, created a question with more than 1,000 views. For Should I get the mean of 2 log2 transformed RPKM values?
Popular Question 17 months ago, created a question with more than 1,000 views. For Cuffdiff not performing tss, cds, splicing, promoter or CDS tests
Popular Question 17 months ago, created a question with more than 1,000 views. For Cuffdiff not performing tss, cds, splicing, promoter or CDS tests
Popular Question 17 months ago, created a question with more than 1,000 views. For Can anyone suggest a RShiny app for displaying RNA-seq results online
Popular Question 18 months ago, created a question with more than 1,000 views. For Meme: What is the optimal sequence length?
Popular Question 18 months ago, created a question with more than 1,000 views. For Meme: What is the optimal sequence length?
Popular Question 19 months ago, created a question with more than 1,000 views. For Meme: What is the optimal sequence length?
Scholar 20 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
Scholar 21 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
Scholar 21 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
Voter 21 months ago, voted more than 100 times.
Popular Question 21 months ago, created a question with more than 1,000 views. For Rshiny - How do I check if user input exists in my data set?
Popular Question 21 months ago, created a question with more than 1,000 views. For Rshiny - How do I check if user input exists in my data set?
Popular Question 21 months ago, created a question with more than 1,000 views. For Quantile normalisation: raw rpkm or log2rpkm?
Popular Question 21 months 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 23 months ago, has more than 80 characters in the information field of the user's profile.
Popular Question 2.0 years ago, created a question with more than 1,000 views. For RNA-seq RPKM significance cut off
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For A: wig files to bigwig using UCSC kent
Guru 2.1 years ago, received more than 100 upvotes.
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