User: sukesh1411

gravatar for sukesh1411
sukesh141130
Reputation:
30
Status:
New User
Location:
South Africa
Last seen:
1 week, 1 day ago
Joined:
2 years, 10 months ago
Email:
s*********@gmail.com

Posts by sukesh1411

<prev • 55 results • page 1 of 6 • next >
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Issue running python script from xampp
... Hi I installed xampp in ubuntu 14.04 to develop a local webserver for performing the variant calling from whole genome data. I wrote a python script to run the variant calling steps and all the script and php files are kept in htdocs folder. I run the python script from webpage by starting xampp. ...
genome next-gen written 6 weeks ago by sukesh141130
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Comment: C: Unable to install SNPhylo in ubuntu
... Thanks for your reply. I tried but it could not find necessary R packages when installing SNPhylo. Please check the error. ![\[1\]: https://imgur.com/a/6oCpO][1] ...
written 7 months ago by sukesh141130
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Unable to install SNPhylo in ubuntu
... Hi I am trying to generate phylogenetic tree for 40 genome rice varieties using SNPhylo program . I could not install SNPhylo program successfully in ubuntu. I could install all the dependent programs except R packages (gdsfmt, SNPRelate). When i try installing these packages manually the packages ...
phylogenetics written 7 months ago by sukesh141130 • updated 7 months ago by leeandroid60
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locus id conversion
... Hi I performed genome annotation for rice using snpeff tool. After annotation, i got locus id information, but not gene id or gene name. Is there any software which can convert the locus id to geneid. I tried most of the softwares in google, but i could not convert the locus id. Sorry i know its a ...
genome annotation written 8 months ago by sukesh141130
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Comment: C: DE analysis using trinity
... Thank you. I could run the script now. I added the path for Fasta_Reader.pm in the script. Thanks ...
written 9 months ago by sukesh141130
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DE analysis using trinity
... Hi I am new to RNA-Seq data analysis. I am using example files, which is given in trinity to perform denovo assembly of rna-seq data. I am struck with the script, run_DE_analysis to perform differential gene expression. when i try to run the script, run_DE_analysis, it gives me below error.. ...
tool rna-seq written 9 months ago by sukesh141130 • updated 9 months ago by Spacebio180
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GC content for RNA-Seq data
... Hi I am new to the rna-seq data analysis. I have rna-seq data of leaf. I would like to perform transcriptome assembly using trinity. Before doing it, i removed the adapters and low quality bases. When i check the quality of reads in FASTQC it shows error for per base sequence content, per base GC c ...
rna-seq written 10 months ago by sukesh141130
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Comment: C: SNP data filtering from VCF file
... Hi Thank you Paul... I finished my job using awk script.. thanks to Pierre :) ...
written 11 months ago by sukesh141130
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Comment: C: SNP data filtering from VCF file
... Hi, I took vcf file from rice 3000 genome project database. Can i use varscan for exporting only snps from vcf file? Thanks ...
written 11 months ago by sukesh141130
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SNP data filtering from VCF file
... Hi I am sorry although there are so many questions on this query i could not find the relavant answer. I used vcftools to extract only snps from vcf file using below command command: vcftools --vcf variantsfilterQDPMQ.vcf --remove-indels --recode --recode-INFO-all --out onlysnps I got the vcf fil ...
snp written 11 months ago by sukesh141130

Latest awards to sukesh1411

Popular Question 6 weeks ago, created a question with more than 1,000 views. For convert text file to fasta file
Popular Question 7 months ago, created a question with more than 1,000 views. For convert text file to fasta file
Popular Question 8 months ago, created a question with more than 1,000 views. For convert text file to fasta file
Popular Question 17 months ago, created a question with more than 1,000 views. For convert text file to fasta file

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