User: YaGalbi
YaGalbi • 1.5k
- Reputation:
- 1,480
- Status:
- Trusted
- Location:
- Biocomputing, MRC Harwell Institute, Oxford, UK
- Website:
- https://github.com/roo...
- Last seen:
- 8 months, 3 weeks ago
- Joined:
- 4 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 >
0
votes
0
answers
474
views
0
answers
... 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 21 months ago by
YaGalbi • 1.5k
0
votes
0
answers
340
views
0
answers
... 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 21 months ago by
YaGalbi • 1.5k
1
vote
0
answers
474
views
0
answers
... 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 21 months ago by
YaGalbi • 1.5k
1
vote
1
answer
1.7k
views
1
answers
... 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 2.0 years ago by
YaGalbi • 1.5k
8
votes
1
answer
1.7k
views
1
answer
... 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 ...
1
vote
1
answer
2.0k
views
1
answers
... Whether a separate run or separate lane makes little difference, they are still technical replicates. They should not be merged. ...
written 2.0 years ago by
YaGalbi • 1.5k
0
votes
2
answers
1.8k
views
2
answers
... 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 2.1 years ago by
YaGalbi • 1.5k
0
votes
2
answers
1.8k
views
2
answers
... "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 2.1 years ago by
YaGalbi • 1.5k
1
vote
0
answers
567
views
0
answers
... Yes, I've started the pipeline for the data, should have the bams tomorrow and the vcfs on friday. thank you. ...
written 2.1 years ago by
YaGalbi • 1.5k
0
votes
0
answers
567
views
0
answers
... exactly what i was thinking - it could be better, but it really isn't that bad. ...
written 2.1 years ago by
YaGalbi • 1.5k
Latest awards to YaGalbi
Appreciated
21 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
21 months ago,
created a question with more than 1,000 views.
For Meme: What is the optimal sequence length?
Popular Question
21 months ago,
created a question with more than 1,000 views.
For CummeRbund: I can't create a dispersion plot - help please?
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 Can anyone suggest a RShiny app for displaying RNA-seq results online
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Nucleoatac - extending broadPeak regions
Popular Question
21 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
21 months ago,
created a question with more than 1,000 views.
For Cuffdiff not performing tss, cds, splicing, promoter or CDS tests
Popular Question
22 months ago,
created a question with more than 1,000 views.
For Cuffdiff not performing tss, cds, splicing, promoter or CDS tests
Popular Question
22 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
23 months ago,
created a question with more than 1,000 views.
For Meme: What is the optimal sequence length?
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Meme: What is the optimal sequence length?
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Meme: What is the optimal sequence length?
Scholar
2.1 years ago,
created an answer that has been accepted.
For C: Displaying genes in genome browsers
Scholar
2.1 years ago,
created an answer that has been accepted.
For C: Displaying genes in genome browsers
Scholar
2.1 years ago,
created an answer that has been accepted.
For C: Displaying genes in genome browsers
Voter
2.1 years ago,
voted more than 100 times.
Popular Question
2.1 years 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
2.1 years 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
2.2 years ago,
created a question with more than 1,000 views.
For Quantile normalisation: raw rpkm or log2rpkm?
Popular Question
2.2 years 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
2.3 years ago,
has more than 80 characters in the information field of the user's profile.
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For RNA-seq RPKM significance cut off
Commentator
2.5 years ago,
created a comment with at least 3 up-votes.
For A: wig files to bigwig using UCSC kent
Guru
2.5 years ago,
received more than 100 upvotes.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 753 users visited in the last hour