925 questions with no upvoted or accepted answers
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### 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 ...
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### 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 ...
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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 ...
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### 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 ...
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### 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: ...
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### 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: ...
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### 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 ...
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### 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 ...
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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 ...
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### 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 ...
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### 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 ...
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### 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 ...
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### 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": ...