User: cschu181
cschu181 • 1.9k
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Posts by cschu181
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... I think that facility desperately needs to review their procedures and you should probably think twice before using them again (if that's an option) If the data is single end, why on Earth would they deliver an R2. Also, if you request paired-end (inferring from your post), why do you get single end ...
written 12 hours ago by
cschu181 • 1.9k
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Comment:
C: single contig de novo assembly
... You can also check the contigs/transcripts that you already have. ...
written 12 hours ago by
cschu181 • 1.9k
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Comment:
C: single contig de novo assembly
... Just a thought: are you certain that all of your RNA-Seq data is pure virus? Have you checked that your other contigs are not something else, e.g. host (depending on how the virus was isolated, obviously)?
I am asking, as I have worked on RNA viruses present in insect transcriptomes. In my case, bo ...
written 14 hours ago by
cschu181 • 1.9k
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... [Earlham Institute][1] has a NovaSeq 6000.
[1]: http://www.earlham.ac.uk ...
written 5 days ago by
cschu181 • 1.9k
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... > What are i and j. Are they just called this because there are paired with each other?
i and j are two bases. They might be called a and b, b_i and b_j or bugs and bunny. i and j are only assumed to be paired with each in case 1 of the scoring function.
> What is K and K + 1 in the bifurca ...
written 11 days ago by
cschu181 • 1.9k
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Comment:
C: Needleman-Wunsch with Python
... For differentiating between gap extension and opening, you need to use an affine gap penalty model. For instance, have a look [here][1].
[1]: http://helios.mi.parisdescartes.fr/~lomn/Cours/BI/Material2019/gap-penalty-gotoh.pdf ...
written 12 days ago by
cschu181 • 1.9k
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... It's not completely clear where your problem is. Is it that you don't know how to do it in Python? I'd say (before one of the others does it), give us some of your ideas and someone might guide you from there. So, if it is just that the Python part is the problem, then outline the steps that you wan ...
written 15 days ago by
cschu181 • 1.9k
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... Just judging from the first couple lines of code at [the CIRIquant github repo][1], the tool will terminate if it doesn't receive -1 and -2, so yea, not without modifying that (which might be easy enough, though!).
[1]: https://github.com/Kevinzjy/CIRIquant/blob/master/CIRIquant/main.py ...
written 18 days ago by
cschu181 • 1.9k
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... Hmm, have you tried to only use the -1 option? ...
written 19 days ago by
cschu181 • 1.9k
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... If this is the published paper (https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-019-0614-1), where do they mention that the program can take in single end reads?
Given that the method is based on (reverse) overlap detection of paired-end reads
> RO read detection and verificati ...
written 20 days ago by
cschu181 • 1.9k
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