User: YaGalbi

gravatar for YaGalbi
YaGalbi1.3k
Reputation:
1,290
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Location:
Biocomputing, MRC Harwell Institute, Oxford, UK
Website:
https://github.com/roo...
Last seen:
an hour ago
Joined:
2 years ago
Email:
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Microbiology BSc Hons 2016

Bioinformatics MSc Distinction 2017

Bioinformatics Prize 2017

Posts by YaGalbi

<prev • 371 results • page 1 of 38 • next >
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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 29 days ago by YaGalbi1.3k
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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 4 weeks ago by YaGalbi1.3k • updated 4 weeks ago by genomax51k
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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 4 weeks ago by YaGalbi1.3k
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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 4 weeks ago by YaGalbi1.3k
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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 4 weeks ago by YaGalbi1.3k
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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 5 weeks ago by YaGalbi1.3k
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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 5 weeks ago by YaGalbi1.3k
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Comment: C: Is the sequence quality good enough?
... Edited ... thank you ...
written 5 weeks ago by YaGalbi1.3k
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Is the sequence quality good enough?
... 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 ...
wgs qc hiseq4000 written 5 weeks ago by YaGalbi1.3k
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Comment: C: Low mapping percentage after mapping RNA-seq reads to a closely related species
... 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 YaGalbi1.3k

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Scholar 6 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
Scholar 7 weeks ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
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Popular Question 9 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?
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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?
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Popular Question 5 months ago, created a question with more than 1,000 views. For RNA-seq RPKM significance cut off
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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
Popular Question 8 months ago, created a question with more than 1,000 views. For RNA-seq RPKM significance cut off
Scholar 8 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
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Scholar 13 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
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