User: haro

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haro220
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Posts by haro

<prev • 85 results • page 1 of 9 • next >
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Comment: C: Read a fasta file | Java
... you can create a class FastaSequence containing the code above, add a 'getHeader' and 'getSequence' and then return only the sequence for your use ...
written 6 weeks ago by haro220
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Answer: A: Read a fasta file | Java
... Hi ozdavidd, you may try this : private void readFastaFile(File fastaFile) { InputStream flux; String line; try { flux = new FileInputStream(fastaFile); InputStreamReader lecture = new InputStreamReader(flux); BufferedReader buff = ne ...
written 6 weeks ago by haro220
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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 3 months 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 3 months 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 3 months 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 3 months 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 3 months 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 3 months 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 3 months 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 3 months ago by haro220

Latest awards to haro

Scholar 7 months ago, created an answer that has been accepted. For A: What is the best way to start learning R?
Scholar 9 months ago, created an answer that has been accepted. For A: What is the best way to start learning R?
Supporter 14 months ago, voted at least 25 times.

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