User: sukesh1411

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sukesh141130
Reputation:
30
Status:
New User
Location:
South Africa
Last seen:
2 weeks, 6 days ago
Joined:
2 years, 3 months ago
Email:
s*********@gmail.com

Posts by sukesh1411

<prev • 54 results • page 1 of 6 • next >
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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 27 days 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 28 days ago by sukesh141130 • updated 26 days ago by Leeandroid v2.920
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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 weeks 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 10 weeks 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 10 weeks ago by sukesh141130 • updated 10 weeks ago by Spacebio80
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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 3 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 4 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 4 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 4 months ago by sukesh141130
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Comment: C: Dealing with CNV overlap
... Hi I am trying to predict the CNVs for three rice genomes using three different softwares like pindel, cnvnator and breakdancer. I would like to know if we find overlap between CNVs reported by two softwares(out of three), should we take only overlapping region for wet lab study or from smallest st ...
written 5 months ago by sukesh141130

Latest awards to sukesh1411

Popular Question 7 weeks ago, created a question with more than 1,000 views. For convert text file to fasta file
Popular Question 10 months ago, created a question with more than 1,000 views. For convert text file to fasta file

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