User: YaGalbi
YaGalbi • 1.4k
- Reputation:
- 1,400
- Status:
- Trusted
- Location:
- Biocomputing, MRC Harwell Institute, Oxford, UK
- Website:
- https://github.com/roo...
- Last seen:
- 5 months, 3 weeks ago
- Joined:
- 2 years, 8 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 5 months ago by
YaGalbi • 1.4k
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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 5 months ago by
YaGalbi • 1.4k
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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 5 months ago by
YaGalbi • 1.4k
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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 9 months ago by
YaGalbi • 1.4k
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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 9 months ago by
YaGalbi • 1.4k
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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 9 months ago by
YaGalbi • 1.4k
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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 9 months ago by
YaGalbi • 1.4k
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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 9 months ago by
YaGalbi • 1.4k
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... exactly what i was thinking - it could be better, but it really isn't that bad. ...
written 9 months ago by
YaGalbi • 1.4k
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