Bioinformatics Stack Exchange
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1500 questions
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votes
3 answers

Getting the licenses of all conda installed packages

I would like to get a list of the licenses of all packages I installed using Conda. pip has what I need in the form of pip-licenses, is there a similar thing for conda?
Freek
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2 answers

How can I convert SCF trace files to ABI files?

I have a large collection of sequence trace files which are in SCF file format (binary files that in addition to the string of DNA bases also contain the electropherogram of the sample and quality information about the base calls). I have an…
BioGeek
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4 answers

What reasons are there to choose Illumina if PacBio provides longer and better reads?

PacBio provides longer read length than Illumina's short-length reads. Longer reads offer better opportunity for genome assembly, structural variant calling. It is not worse than short reads for calling SNP/indels, quantifying transcripts. Sounds…
SmallChess
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1 answer

Highly heterozygous reads mapping

I have short (67bp) Hi-C reads from a highly heterozygous organism (~15% between-haplotype SNP divergence) and I have both reference haplotypes. I wanted to try and compare different haplotyping softwares for Hi-C reads using these reads as…
cmdoret
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7 answers

What are the available cloud computing services for bioinformatics?

I'm looking for cloud computing services that can be used for doing bioinformatics. An example I found is InsideDNA and there is Amazon of course. A little description of these would be appreciated.
Peter
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8
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2 answers

Getting structure and sequence related to PDB IDs

I have two kinds of interactions: transient and stable. We are supposed to work on stable interaction, like interactions between two monomers in a heterodimer. In a heterodimer there are two chains in which there are some residues between monomers…
Sara
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8
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3 answers

How to detect a mutation and predict its consequence?

I read lecture notes about mutations, and wondered what kind of algorithms are there to detect mutations? How do we know if the gene is mutated or whether it is a sequencing error? I saw this thread which is related, but I am not sure how to use the…
0x90
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8
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2 answers

What is mate rescue in bwa mem?

BWA mem has the -S and -P tags for skip mate rescue and skip pairing; mate rescue performed unless -S also in use. What do these do? I presume -P aligns read pairs independently of each other. Is that correct? And what does -S do?
juniper-
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1 answer

What are "split reads" and "intron clusters?"

I'm working through the example data set for LeafCutter and the documentation mentions "split reads": This will cluster together the introns fond [sic] in the junc files listed in test_juncfiles.txt, requiring 50 split reads supporting each …
CelineDion
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0 answers

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 via scanBam in different windows (which…
Konrad Rudolph
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1 answer

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 coordinates and found that a lot of them overlap with…
Alex Stuckel
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1 answer

How is prior.count used by edgeR's cpm

edgeR's cpm function has an argument called prior.count. Based on my understanding of the documentation, it is supposed to be adding a fixed number per sample which is proportional to the library size of said sample. Average of all numbers added to…
OganM
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8
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2 answers

Running SnakeMake on cluster

I do not understand how to specify correctly the parameters on a SLURM cluster for snakemake to use them. I tried submitting the following SLURM file, but it does not work this way and the number of cores used is only 1, not 20: #!/bin/bash #SBATCH…
Nikita Vlasenko
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8
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2 answers

Are these standard species abbreviations and how to look up others?

Reactome uses a three letter code for each species which are listed below. Are the letter codes used by Reactome a standard? If so is there a web page or download file that can validate the code and translate it to a common name? HSA Homo sapiens …
Guy Coder
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8
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2 answers

estimate genome size: kmer-based approach from PacBio reads

Can anyone suggest a software/method for kmer analysis using PacBio reads (RSII)? Something similar to Jellyfish, that I saw in a nice tutorial - but must be suitable for long, noisy reads. kmercounterexact from BBMapTools might also be an option,…
aechchiki
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