Unanswered Questions
1,093 questions with no upvoted or accepted answers
9
votes
0
answers
141
views
Run cuffcompare in strand-agnostic mode
Is there a way to run Cufflinks' cuffcompare in a strand-agnostic mode?
I would like to do this because I have some RNA-seq datasets derived from an unstranded run, that should be compared to a ...
- 19.6k
8
votes
0
answers
462
views
How can I read multiple different regions from a BAM file in R?
I’m trying to process BAM records (of a coordinate-sorted, indexed BAM file) successively in fixed-size, non-overlapping, sliding genome coordinate windows. Unfortunately I am unable to read records ...
- 13.8k
6
votes
0
answers
302
views
Using dssp after chain extraction
I have a list of PDB IDs with realtive chains IDs that have to be extracted, and then run on dssp.
For the single chain extraction I tried several methods, such as:
...
- 955
6
votes
0
answers
64
views
Why does repeatmasker annotate transposons of length 1?
I am working on Mac OSX. I have downloaded RepeatMasker from www.repeatmasker.org. I have downloaded RepBase from www.girinst.org. I have download the WS266 version of the C. elegans genome from ...
- 13.8k
6
votes
0
answers
977
views
changing blast parameters using NCBIWWW module
I have found a blog post with a script that I would like to use for my current research project: link
The script is incredibly fast and produces a smooth conservation plot. In the blog post, the ...
M__♦
- 11.9k
6
votes
1
answer
597
views
Download data from the Human Microbiome Project via ascp
I have asked this question in biostars, but I am trying here as well as people working with "omics" data might be able to help. I think my issue relates understanding how large data storage on online ...
CommunityBot
- 1
5
votes
1
answer
212
views
UPGMA computation
The unweighted pair group method with arithmetic mean (UPGMA) is a hierarchical clustering method, for example used in phylogeny. In a phylogenetic tree it would result in a global molecular clock ...
CommunityBot
- 1
5
votes
0
answers
163
views
Simultaneously get data from multiple applied gates in flowCore
Using the Bioconductor flowCore package, I'm applying two parallel and non-overlapping gates to a gatingSet directly under "root":
...
- 183
5
votes
0
answers
51
views
Parse RNA variant effect annotations ("r." format)
I've got annotations for splicing variants in a format like this (this is one variant):
Variant: NM_004092.3:c.88+5G>A
Effect: Retention; r.87_88ins1_88+10:p.(Ala31Glufs*23)
I want to extract ...
M__♦
- 11.9k
5
votes
0
answers
354
views
What exactly does each of InterPro, PANTHER, Pfam bring to the table individually in classifying a protein?
I would be very grateful if somebody could sketch out the methods Pfam and PANTHER use to assign a family to a given protein and how they are different. My (cursory) understanding is that InterpProp ...
M__♦
- 11.9k
5
votes
0
answers
30
views
Iupred definition of long/short form disorder
I need to predict disorder of proteins and here there is a description of Iupred in its two variants, long and short-disorder. This is a manuscript defining the method. I couldn't find a precise ...
- 9,662
5
votes
0
answers
85
views
What is a sensible forcefield choice for membrane proteins when using PDB2PQR?
I am generating PQR files for a membrane protein that is almost entirely buried in the membrane. The goal is to calculate the electrostatic charge across the surface of the protein. There are no ...
M__♦
- 11.9k
5
votes
0
answers
225
views
convert supplementary reads to primary in sam or bam
I have a problem with a tool, that possibly ignores supplementary reads. I want to find out a bit how this tool works by converting all supplementary reads to primary reads, and then change the names ...
- 13.8k
5
votes
0
answers
81
views
Database of Cell Volumes by Cell Ontology?
Are there any databases that have aggregated information on cell volumes? Most useful would be a database keyed by cell ontology (e.g., CL:0000236 for B cell).
...
M__♦
- 11.9k
5
votes
0
answers
55
views
Gathering data on bacterial oganism growth conditions
let's say I have a list of organism names like the example below
...
- 13.8k