Bioinformatics Questions, Problems & Solutions : TransWikia.com ~ Page 28

WGBS vs ONT, which one should I trust?

First of all let me apologize if this is not the place for this question. While it can be quite broad, I will try to make it as specific as...

Asked on 04/14/2021

2 answer

How to tell which channel is the reference channel in two channel (red green) array data?

I'm sorry if this is a stupid question - I have not analysed two channel array data before. I have a GenePix data file, which does not seem to indicate...

Asked on 04/14/2021 by Heather Harrington

1 answer

Given a .gb file and a locus - how to get relevant annotations in Python?

Given a .gb file and a specific locus in the genome - how can I retrieve the relevant annotations in Python (i.e., annotations that include that locus)? I could...

Asked on 04/13/2021

1 answer

How to retrieve the DNA sequence from a particular species and region through command line?

I am new to working with the NCBI database so I am not sure how trivial this question is. I wanted to get DNA sequence of a specific version of...

Asked on 04/13/2021 by fp1234

2 answer

plink: --update-name vs. editing the BIM

I am working with data from the HGDP public files. These are massive VCFs from whole genome sequencing. To begin with, I converted these to BEDs using...

Asked on 04/11/2021 by CoderGuy123

2 answer

Extract residue sequence from pdb file (in biopython, but open to recommendations)

I'm new to Biopython and I'd like to extract the sequence of residues from a pdb file. My two questions are:What is the simplest way to do this? (Esp. when...

Asked on 04/11/2021 by mzzx

4 answer

Is there a way to know whether the genome in the NCBI genome database is from type strain?

Is there a method to check whether 1000 genomes downloaded from the NCBI genome database are from type strains? Best regards,Yanpeng Chen...

Asked on 04/10/2021

0 answer

About getting rs id from chromosome and position

Hi I have a dataset with chromosome and position.VARIANT_ID chromosome position17_26797415_147499 17 2679741517_26797556_147500 17 26797556 How can I assign rs...

Asked on 04/10/2021 by susuauidikd

0 answer

Biopython BioSQL error : AttributeError: 'DBSeq' object has no attribute '_data'

Hi I am playing with Biopython and BioSQL, I manage to create an MySQL database using Managing local biological databases with the BioSQL module tutorial: and load...

Asked on 04/09/2021 by pippo1980

1 answer

How to convert a Pileup file to VCF format with Hg19 alignment

I would like to know how to convert a pileup file for an adna y chromosome to vcf with Hg19 alignment....

Asked on 04/09/2021 by Samir Bouftass

1 answer

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