User: mrals89

gravatar for mrals89
mrals8950
Reputation:
50
Status:
Trusted
Location:
United States
Last seen:
5 months, 3 weeks ago
Joined:
6 years, 4 months ago
Email:
m******@gmail.com

about me

Posts by mrals89

<prev • 19 results • page 1 of 2 • next >
0
votes
0
answers
246
views
0
answers
How to write a BGZF file with Biopython?
... Hi everyone, I've read the documentation for [`Bio.bgzf`](https://biopython.org/DIST/docs/api/Bio.bgzf-module.html) and I'm sufficiently confused by it. To create an example bgzf file, I've tried the following. The [`write`](https://github.com/biopython/biopython/blob/cfb26444d0c84fa5d0aa8f1ed8979 ...
bgzf biopython written 7 months ago by mrals8950
1
vote
1
answer
343
views
1
answers
Comment: C: what is the best way to calculate significant differences in tss profiles?
... Echoing ATpoint for a second, you are trying to test for differences between singletons, which isn't possible base-by-base between singletons. You require replicates measurements of coverage in order to do a KS-test or something similar. A p-value isn't a very strong statistic, since 'coverage' valu ...
written 12 months ago by mrals8950
0
votes
0
answers
217
views
0
answers
Comment: C: Linear Modelling In Systems Biology help
... I think you should start with the biological process you want to model. If you don't have something you wish to model, then you should start with 'Mathematical Biology' which is a great introduction to application of growth rates and system dynamics to biology. A 2x1 or 1x1 system may *seem* trivial ...
written 12 months ago by mrals8950
0
votes
0
answers
292
views
0
answers
Comment: C: Is it possible to transfer a local instance of Galaxy (from my computer) to Clou
... What is the command line you're using for hisat? Also, moving the indices, references, and tools into AWS is a considerable effort. If you're looking to just run a one-off analysis, you're better off launching a cloud instance, SSH-ing into the instance and performing your analysis there than settin ...
written 12 months ago by mrals8950
0
votes
1
answer
778
views
1
answers
Answer: A: Distance of promoter from TSS
... Hello there. I'd say that you're focusing your efforts on a single gene. The question you asked is, how unlikely is the promoter sequence's distance? That is a bioinformatics question certainly. To 'guestimate' whether this anwer is reasonable you'd need data on promoter locations across many genes, ...
written 12 months ago by mrals8950
0
votes
0
answers
1.8k
views
0
answers
Comment: C: Any packages to validate FASTA file?
... If you need empty records to be considered invalid, maybe you could issue a pull request to biopython ...
written 18 months ago by mrals8950
0
votes
7
answers
6.1k
views
7
answers
Comment: C: Modern software for whole genome alignment visualization
... Compare in what way, sir? Are you looking at rearrangements? CNVs? Or are you interested in homology and sequence features? ...
written 2.2 years ago by mrals8950
0
votes
2
answers
602
views
2
answers
Answer: A: Looking for a local alignment library with certain features
... From your comment to @ATpoint, it seems like you're looking for 'long' read alignment algorithms. I'd suggest BWA-mem for that (it seems to be the conventional wisdom). But OP, it's not clear why you 'cant have indexes or many I/O operations.' Because BLAST uses indices!! I can't tell if you're tr ...
written 2.2 years ago by mrals8950
1
vote
7
answers
6.1k
views
7
answers
Comment: C: Modern software for whole genome alignment visualization
... I think there's a separation of concerns issue here OP. Genome browsers are typically responsible for loading BAM, fasta, and BED annotations, maybe vcfs. They are a data exploration application. Ability to extract variants... you mean predict from the BAM files? Or you mean export the loaded vcfs ...
written 2.2 years ago by mrals8950
0
votes
2
answers
1.3k
views
2
answers
Comment: C: How to download sequences of one gene from all individuals from 1000 genome (pha
... This is a simpler approach to study the SNPs than just slicing the gene from the BAM files or assemblies, OP. ...
written 2.2 years ago by mrals8950

Latest awards to mrals89

Popular Question 3.1 years ago, created a question with more than 1,000 views. For Does Every Read In Paired-End Sam File Have The 0X0001 Flag?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Directional Rnaseq: Which Mapping Software For Bacteria?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1009 users visited in the last hour