Unanswered Questions

925 questions with no upvoted or accepted answers
9 votes
0 answers
127 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
351 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 ...
7 votes
0 answers
57 views

Gene not found in Affymetrix expression profiles

I am studying the ABA network in A. thaliana, consisting of HB7, ABI1 and AREB2. The AGI code I was given are, respectively: AT2G46680, AT4G26080 and AT1G45249. I downloaded the following file in ...
7 votes
0 answers
32 views

dog coordinates (canFam3) to human coordinates (hg19)

I've converted dog coordinates to human using UCSC LiftOver*. These are 200bp intergenic regions that are differentially methylated from normal dogs to cancer dogs. I've converted these to human ...
6 votes
0 answers
139 views

Using dssp after chain extraction

I have a list of PDB IDs with realtive chains that are to be extracted, and the run on dssp. For the single chain extraction I tried several methods, such as: ...
6 votes
1 answer
100 views

What does it mean if aligned genomes are not of the same length?

I am aligning 4 genomes of Psuedomonas chlororaphis using progressive mauve software. Command used: ...
6 votes
1 answer
516 views

lower mapping rates in salmon v0.13 compared to previous versions

Hi there :) Thanks for the tool! I recently updated to the new salmon (from 0.8... its been a couple years) and I noticed that my mapping percentages change dramatically between the two versions. For ...
6 votes
0 answers
60 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
780 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
491 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
0 answers
41 views

Where to find asymmetric nucleotide substitution matrix with IUPAC encodings?

I am using the pairwiseAlignment function from the Biostrings package to calculate the distance between a consensus sequence and ...
5 votes
1 answer
178 views

Is there any function in Biopython to convert a DNA sequence from ambiguous to unambiguous?

I have a project to write in Python that requires to write a function that given degenerate DNA sequence (for example: KKGTACACCAG) sequence and a molecular weight interval, returns a list of all ...
5 votes
1 answer
45 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
82 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
201 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 ...

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