User: YaGalbi

gravatar for YaGalbi
YaGalbi1.4k
Reputation:
1,420
Status:
Trusted
Location:
Biocomputing, MRC Harwell Institute, Oxford, UK
Website:
https://github.com/roo...
Last seen:
10 months ago
Joined:
3 years 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 10 months ago by YaGalbi1.4k
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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 10 months ago by YaGalbi1.4k
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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 10 months ago by YaGalbi1.4k
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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 13 months ago by YaGalbi1.4k
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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 13 months ago by YaGalbi1.4k • updated 13 months ago by genomax70k
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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 13 months ago by YaGalbi1.4k
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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 13 months ago by YaGalbi1.4k
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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 13 months ago by YaGalbi1.4k
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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 13 months ago by YaGalbi1.4k
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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 13 months ago by YaGalbi1.4k

Latest awards to YaGalbi

Popular Question 10 months ago, created a question with more than 1,000 views. For Cuffdiff not performing tss, cds, splicing, promoter or CDS tests
Popular Question 10 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 11 months ago, created a question with more than 1,000 views. For Meme: What is the optimal sequence length?
Popular Question 11 months ago, created a question with more than 1,000 views. For Meme: What is the optimal sequence length?
Popular Question 12 months ago, created a question with more than 1,000 views. For Meme: What is the optimal sequence length?
Scholar 13 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
Scholar 13 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
Scholar 13 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
Voter 14 months ago, voted more than 100 times.
Popular Question 14 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 14 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 14 months ago, created a question with more than 1,000 views. For Quantile normalisation: raw rpkm or log2rpkm?
Popular Question 14 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 16 months ago, has more than 80 characters in the information field of the user's profile.
Popular Question 17 months ago, created a question with more than 1,000 views. For RNA-seq RPKM significance cut off
Commentator 18 months ago, created a comment with at least 3 up-votes. For A: wig files to bigwig using UCSC kent
Guru 18 months ago, received more than 100 upvotes.
Scholar 20 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
Scholar 20 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
Popular Question 20 months ago, created a question with more than 1,000 views. For RNA-seq RPKM significance cut off
Scholar 20 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
Popular Question 2.1 years ago, created a question with more than 1,000 views. For RNA-seq RPKM significance cut off
Scholar 2.1 years ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Looking for an annotation tool
Student 2.1 years ago, asked a question with at least 3 up-votes. For Is annotation of enhancers to nearest gene pointless?

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