User: haro

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haro220
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Posts by haro

<prev • 83 results • page 1 of 9 • next >
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Answer: A: shannon entropy score
... Give a try to biojava: import java.util.*; import org.biojava.bio.dist.*; import org.biojava.bio.seq.*; import org.biojava.bio.symbol.*; public class Entropy { public static void main(String[] args) { Distribution dist = null; try { //crea ...
written 10 days ago by haro220
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Answer: A: Mean coverage in Ion Torrent PGM
... Hi Abdul Rafay Khan, You can use samtools depth: samtools depth -b file.bed -a file.bam > coverage.csv Also, a plugin named 'coverageAnalysis' exists directly on the Proton machine ...
written 11 days ago by haro220
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How to display differences after biojava alignment?
... Hi! I would like to compare 2 dna sequences and display the differences in nucleic acids on a screen **and then** convert this/these particular difference(s) in codons. Here is how I display the alignment, I'm a little bit confuse on what to do on the following steps private void alignment() ...
biojava alignment written 16 days ago by haro220
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Comment: C: Reference Genome for mapping and VCF file for Realignment in Yak (Bos grunniens)
... you can download fastq files by ftp and do yourself a consensus sequence or use the whole genome shotgun sequences available from genebank ...
written 16 days ago by haro220
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Comment: C: Reference Genome for mapping and VCF file for Realignment in Yak (Bos grunniens)
... ok check the links from the answer I just posted for the references. You have to generate your own vcf... What exactly are you looking for? and what kind of data do you have to start? ...
written 16 days ago by haro220
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Answer: A: Reference Genome for mapping and VCF file for Realignment in Yak (Bos grunniens)
... ok from this [study][1] you have the data accessible [here][2]. Otherwise, whole genome shotgun sequences are available from the genebank : [here][3] [1]: https://www.nature.com/articles/ncomms10283 [2]: https://www.ebi.ac.uk/ena/data/view/PRJNA285834 [3]: https://www.ncbi.nlm.nih.gov/nuccor ...
written 16 days ago by haro220
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Comment: C: Reference Genome for mapping and VCF file for Realignment in Yak (Bos grunniens)
... Can you be more specific on what you are looking for? variant calling from specific gene, complete genome... What kind of data do you have? You may find a reference sequences on the [genebank][1] [1]: https://www.ncbi.nlm.nih.gov/nuccore/?term=Bos%20grunniens ...
written 16 days ago by haro220
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Answer: A: Tools For Metagenomic Data Analysis
... Have a look on [Mash Screen][1], I found it usefull and easy to use! [1]: https://genomeinformatics.github.io/mash-screen/ ...
written 16 days ago by haro220
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Answer: A: Any returns on plasmidSPAdes?
... Ok, to be more accurate, I'm trying to determine if an antibiotic resistance gene is whether on the chromosome or in a plasmid of a bacteria. I tried different approaches and I saw that SPAdes was able to generate plasmids, I tried but was quiet disappointed; I have a strain containing the resista ...
written 5 weeks ago by haro220
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Comment: C: How to retrieve all pentamer from a sequence?
... this software is awesome, that's exactly what I was looking for, you made my day!! ...
written 6 weeks ago by haro220

Latest awards to haro

Scholar 4 months ago, created an answer that has been accepted. For A: What is the best way to start learning R?
Scholar 6 months ago, created an answer that has been accepted. For A: What is the best way to start learning R?
Supporter 11 months ago, voted at least 25 times.

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