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Bioinformatics : Recent Questions and Answers (Page 39)

Find answers to your questions about Bioinformatics or help others by answering their Bioinformatics questions.

Generating 3D coordinates error

I have been trying to convert a multi entry sdf file to pdb using openbabel. Everytime I check the Generate 3D coordinates box I end up with .ENT files instead...

Asked on 01/15/2021 by Shahbaaz

1 answer

Save output to a specific folder and/or with a specific prefix in Cancer Genomics Cloud

I would like to run the CNVkit workflow on Cancer Genomics Cloud. However, the two workflows that I'd like to use:CNVkit Reference, for building...

Asked on 01/15/2021

1 answer

Populations genetics and dynamics of bacteria on a Graph

Disclaimer: I'm a physicist and I'm fairly new to Bioinformatics therefore somethings below may not make sense.My purpose: I would like to simulate genetic evolution of bacterial populations, implementing...

Asked on 01/13/2021

1 answer

Convert a fasta file to Newick format

My problem is (should be) pretty simple. I have a series of 10 sequences which I wish to convert into a Newick format file - what would be good software...

Asked on 01/11/2021

3 answer

BAM file filteing to remain best isoform

I ran HiSat2, MarkDuplicate, removed reads with the lower quality score than 40 and finally only kept properly paired reads. After the BAM filtering steps, I used the Scallop results...

Asked on 01/10/2021 by user977828

0 answer

How is the GT field in a VCF file defined?

As my question in SO was closed and asked to be posted in this forum, I am posting it here I am not from the bioinformatics domain. However, for...

Asked on 01/07/2021

2 answer

Somatic mutations for normal WES samples

I am trying to identify somatic mutations on healthy subjects (specifically in WES samples). As of now, I have found a couple of papers who have done similar studies such...

Asked on 01/06/2021 by Lot_to_learn

0 answer

Get list of urls of GSM data set of a GSE set

I have this GSE dataset ( GSE104279 ) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104279). I want to make a table with set IDs and ftp urls to use it as a table...

Asked on 01/06/2021 by user432797

1 answer

Why is there a chloride ion in this 3D model?

Here we have a 3D model of a sequence that match with this sequenceVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKin Blast the 3D structure is here Why is there a chloride...

Asked on 01/04/2021 by Manuel Milla

1 answer

Biohackers Netflix - DNA to binary and video

I'm not sponsored or anything, just interested in their challenge to decipher their DNA code. They encoded their first episode of "Biohackers" video/binary file to DNA code and said if...

Asked on 01/03/2021 by xamax

1 answer

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