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Unanswered Questions

1,171 questions with no upvoted or accepted answers
9 votes
0 answers
147 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 ...
8 votes
0 answers
486 views

How can I read multiple different regions from a BAM file in R?

Iā€™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 ...
6 votes
0 answers
337 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: ...
6 votes
0 answers
65 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 ...
6 votes
0 answers
1k 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 ...
6 votes
1 answer
615 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 ...
5 votes
1 answer
230 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 ...
5 votes
0 answers
174 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": ...
5 votes
0 answers
53 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 ...
5 votes
0 answers
403 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 ...
5 votes
0 answers
31 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 ...
5 votes
0 answers
87 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 ...
5 votes
0 answers
244 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 ...
5 votes
0 answers
83 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). ...
5 votes
0 answers
333 views

Annotating splice junctions from tophat/STAR output

Is there a way to annotate the splice junctions output from tophat/STAR output? What I mean by annotate is can I know if it was involved in an alternative splicing event say skipped exon, MXE or ...

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