6
votes
Accepted
What is the distribution of indel sizes in a healthy human genome? of insertion:deletion ratios?
One of the 2015 papers from the 1000 genomes project has a nice figure (figure 1) showing the size distribution of medium to large sized insertions and deletions:
From another 2015 1000 genomes paper,...
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5
votes
What is the distribution of indel sizes in a healthy human genome? of insertion:deletion ratios?
Genome-In-A-Bottle (GIAB; version 3.3.2) contains 3.21M SNPs on auto+X chromosomes and 0.51M INDELs in 2.58Gb confident regions. The ins:del ratio is 0.92. On the CHM1-CHM13 pacbio assembly (European ...
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4
votes
Books on bioinformatics algorithms
Here are a couple books I'd recommend:
Dan Gusfield's Algorithms on Strings, Trees, and Sequences is a deep and wide treatment of aligning, searching, and processing strings, trees, and sequences.
...
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4
votes
Accepted
Influential papers in bioinformatics
Over on biostars there's a thread like this every year or so. I'll link to the 2016 edition and the (much shorter) 2015 edition.
My personal picks from those would be:
ExAC
salmon, which is now ...
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4
votes
Fast and reliable alternatives to blast
As I understand, the software tool Lambda is a viable, yet lesser known alternative to BLAST in the context of taxonomic classification of NGS data.
4
votes
Fast and reliable alternatives to blast
Besides generic nucleotide aligners, there are also more specialized tools for the alignment of 16S amplicon sequences, e.g. SINA (article, software) which is part of SILVA
- 443
4
votes
Concerning the current outbreak, using bioinformatics
My personal approach to something like this is to first try to reproduce existing work in order to learn to use relevant tools and understand the concepts involved. Then as you get more comfortable ...
3
votes
Appropriate value to replace outliers in clinical studies
In my experience, it is more common to use all clinical data as-is for clinical studies. And if data is missing, either omit the sample or omit the variable with missing data.
If your classifier can'...
- 367
3
votes
Books on bioinformatics algorithms
If you're interested in variant calling, I just co-authored an O'Reilly book called Genomics in the Cloud that covers the GATK Best Practices from a scientific standpoint (germline and somatic short ...
3
votes
Books on bioinformatics algorithms
Bioinformatics and Functional Genomics by Jonathan Pevsner is a good one, he goes over the biology as well as how the algorithms work, and provides real-world examples.
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3
votes
Accepted
Build a Pubmed query given long gene list
After getting it out on paper (so to speak) I was able to accomplish what I wished with bash:
...
- 1,149
2
votes
How can I export all and only the publications cited by a specific article?
Something like this will work, it did just now for me. You might want to extract different info from the records though.
This exports to a table (bibliography.tsv) columns containing:
pmid
authors
...
2
votes
Protein misfolding
Excellent question! I would recommend that you start with an NIH resource at the National Library of Medicine (NLM). PubMed (https://pubmed.ncbi.nlm.nih.gov/) provides search capabilities across the ...
- 123
2
votes
Concerning the current outbreak, using bioinformatics
Please note that Cuvid19 is COVID-19, the WHO nomenclature. SARS2 is specifically called SARS-CoV-2 and is the virologists name for COVID-19 because that is the nomenclature of the International ...
M__♦
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2
votes
How to calculate Moreau-Broto autocorrelation, Moran autocorrelation, Geary autocorrelation from protein (amino acid) sequences?
Rajarshi Guha describes the formulas to calculate Moreau Broto autocorrelation, Moran coefficient and Geary coefficient and has a bibliography.
But why reinvent the wheel? It seems that the ...
- 496
2
votes
Accepted
Error correction within the long read
Yes, there is a tool to do this called R2C2 by the Vollmers lab at UC Santa Cruz.
https://www.biorxiv.org/content/early/2018/06/04/338020
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2
votes
how to search NCBI to find all available reviewed accession numbers for a protein family
A simple approach is to search for the gene name in NCBI Gene portal but this can miss a few cases and often include genes that are unrelated because the gene symbol is used by other unrelated genes ...
- 1,286
2
votes
Merging transcriptomes coming from different experiments
As mentioned in the comments, your biological question is going to be vitally important in determining the best way to tackle this issue. However, there are some things that you should generally keep ...
- 316
1
vote
Appropriate value to replace outliers in clinical studies
Removing outliers is common practice in statistical modeling and perfectly acceptable. However, with regards 1.5 IQR I am far from certain about this approach. Normally, if you want to be conservative ...
M__♦
- 13k
1
vote
Replicate papers (beginner)
Bioinformatics is a big and very heterogeneous field with a lot of variation, so it's hard to recommend something that covers everything. That said, I think the best you'll do is to build familiarity ...
- 4,262
1
vote
Attractor Landscape Analysis
From Wikipedia:
In the mathematical field of dynamical systems, an attractor is a set of numerical values toward which a system tends to evolve, for a wide variety of starting conditions of the system....
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