User: YaGalbi
YaGalbi • 1.5k
- Reputation:
- 1,500
- Status:
- Trusted
- Location:
- Biocomputing, MRC Harwell Institute, Oxford, UK
- Website:
- https://github.com/roo...
- Last seen:
- 1 year ago
- Joined:
- 4 years, 3 months ago
- Email:
- r**********@gmail.com
Microbiology BSc Hons 2016
Bioinformatics MSc Distinction 2017
Bioinformatics Prize 2017
Posts by YaGalbi
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... 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 2.1 years ago by
YaGalbi • 1.5k
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... 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 2.1 years ago by
YaGalbi • 1.5k
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... 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 2.1 years ago by
YaGalbi • 1.5k
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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 2.4 years ago by
YaGalbi • 1.5k
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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 2.4 years ago by
YaGalbi • 1.5k
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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 2.4 years ago by
YaGalbi • 1.5k
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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 2.4 years ago by
YaGalbi • 1.5k
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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 2.4 years ago by
YaGalbi • 1.5k
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... exactly what i was thinking - it could be better, but it really isn't that bad. ...
written 2.4 years ago by
YaGalbi • 1.5k
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