User: george.ry
george.ry • 1.1k
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Posts by george.ry
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... There's a variety of things at play here, but a few main things. Others can probably add some extra considerations.
- Phased gene expression. RNA is not produced constantly and in an even manner. If I remember correctly, the idea of scRNAseq comes from studies of transcriptional regulation, rath ...
written 11 months ago by
george.ry • 1.1k
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... Get [datamash][1] ... it's invaluable!
`sort -k1,1 < inputfile | datamash -g1 collapse 2 > groups`
[1]: https://www.gnu.org/software/datamash/ ...
written 11 months ago by
george.ry • 1.1k
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... For how many leaf nodes then, outside of this example dataset? ...
written 11 months ago by
george.ry • 1.1k
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2.9k
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... You can also have a look at [UGENE][1] as an alternative to Geneious.
[1]: http://ugene.net/ ...
written 11 months ago by
george.ry • 1.1k
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... Before you get too involved you need to make sure what you're planning is practical, as you get a lot of bifurcating trees from surprisingly few leaf nodes (and if it's bifurcating + others then it's even worse). If your plan is to do some compute for goodness of fit etc on all of these, then you m ...
written 11 months ago by
george.ry • 1.1k
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1
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... from collections import defaultdict as dd
from Bio import SeqIO
import numpy as np
shuffles = dd(list)
for record in SeqIO.parse(open('firstperm.fasta'), 'fasta'):
id = record.id.split('_')[0]
shuffles[id].append(len(record))
for k, v in shuffles.items( ...
written 11 months ago by
george.ry • 1.1k
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2
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912
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... This is technically an issue with a malformed GTF due to the GFF-->GTF conversion, rather than with the script per se - the GTF format is defined [here][1], and should always include `gene_id` and `transcript_id` (it should also end each line with a ';' character).
It'll be simplest to just repl ...
written 11 months ago by
george.ry • 1.1k
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2
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453
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2
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Comment:
C: Print line based on partial match
... It definitely will work, but you have to put `^` in front of the 5 letter sequences in `File1` ...
^ATGCC
^TTGCA
^GGAAC
If you don't want to use grep then any program that will separate based on user-defined barcodes - flexbar / etc - will do this for you. ...
written 12 months ago by
george.ry • 1.1k
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1
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480
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... If you're not looking to call the variants as Medhat says, then [bam-readcount][1] will do this.
[1]: https://github.com/genome/bam-readcount ...
written 12 months ago by
george.ry • 1.1k
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4
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... This isn't your problem I don't think ... the package isn't handling it's own imports properly. You probably just need to change `from . import get_version` to `from GFFUtils import get_version`.
The program isn't doing anything particularly exciting anyway, though, so you could also just do it in ...
written 20 months ago by
george.ry • 1.1k
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