User: george.ry

gravatar for george.ry
george.ry1.1k
Reputation:
1,090
Status:
Trusted
Location:
United Kingdom
Last seen:
4 days, 10 hours ago
Joined:
5 years, 7 months ago
Email:
g********@gmail.com

Posts by george.ry

<prev • 96 results • page 1 of 10 • next >
3
votes
3
answers
1.4k
views
3
answers
Answer: A: What is the actual cause of excessive zeroes in single cell RNA-seq data? Is it
... 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 21 months ago by george.ry1.1k
0
votes
2
answers
707
views
2
answers
Answer: A: problem in fetching data using excel
... Get [datamash][1] ... it's invaluable! `sort -k1,1 < inputfile | datamash -g1 collapse 2 > groups` [1]: https://www.gnu.org/software/datamash/ ...
written 21 months ago by george.ry1.1k
1
vote
0
answers
1.2k
views
0
answers
Comment: C: How do I generate all possible Newick Tree permutations for a set of species giv
... For how many leaf nodes then, outside of this example dataset? ...
written 21 months ago by george.ry1.1k
3
votes
3
answers
5.8k
views
3
answers
Answer: A: Any alternative (free, open source tool) for Geneious software for phylogenetic
... You can also have a look at [UGENE][1] as an alternative to Geneious. [1]: http://ugene.net/ ...
written 21 months ago by george.ry1.1k
1
vote
0
answers
1.2k
views
0
answers
Comment: C: How do I generate all possible Newick Tree permutations for a set of species giv
... 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 21 months ago by george.ry1.1k
1
vote
1
answer
604
views
1
answers
Answer: A: Computing chunk of fasta file before moving to next chunks using python
... 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 21 months ago by george.ry1.1k
0
votes
2
answers
1.6k
views
2
answers
Comment: C: How to Run the Script for Extracting Splice Sites from the Gene Annotation File
... 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 21 months ago by george.ry1.1k
0
votes
2
answers
653
views
2
answers
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 22 months ago by george.ry1.1k
0
votes
1
answer
751
views
1
answers
Answer: A: frequency of each nucleotide at each position in sequence
... 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 22 months ago by george.ry1.1k
1
vote
4
answers
4.9k
views
4
answers
Answer: A: Run a Python program in Ubuntu
... 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 2.5 years ago by george.ry1.1k

Latest awards to george.ry

Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Teacher 10 months ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Appreciated 15 months ago, created a post with more than 5 votes. For A: Help for changing fasta seq ID
Guru 21 months ago, received more than 100 upvotes.
Scholar 21 months ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Scholar 21 months ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Scholar 2.6 years ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Scholar 2.6 years ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Commentator 2.8 years ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Scholar 3.4 years ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Pundit 3.7 years ago, created a comment with more than 10 votes. For C: Do bioinformaticians often break molecular biologists' hearts by being the first
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Help for changing fasta seq ID
Commentator 3.7 years ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Supporter 3.7 years ago, voted at least 25 times.
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Help for changing fasta seq ID
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Scholar 4.1 years ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Commentator 4.1 years ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Commentator 4.1 years ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Scholar 4.3 years ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1165 users visited in the last hour