User: sukesh1411

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sukesh141130
Reputation:
30
Status:
New User
Location:
South Africa
Last seen:
3 days, 13 hours ago
Joined:
2 years ago
Email:
s*********@gmail.com

Posts by sukesh1411

<prev • 51 results • page 1 of 6 • next >
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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 11 days 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 11 days ago by sukesh141130 • updated 11 days 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 4 weeks 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 9 weeks 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 9 weeks 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 9 weeks 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 12 weeks ago by sukesh141130
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Comment: C: Blast standalone output formatting
... Hi The command used for tblastn tblastn -query allpeptide.fa -subject BDCS01.1.fsa_nt -outfmt 0 > results.txt. In 6 or 7 format i can export the results into excel and sort it based on the percentage identity, but in these formats i cant visualize the pairwise alignment results. output file ...
written 4 months ago by sukesh141130
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Blast standalone output formatting
... Hi, I am running tblastn standalone in ubuntu. I wanted to sort the output format 0 (pairwise)using percentage identity. I am able to do this with output format 6 or 7, but not with 0. Thanks ...
tool blast written 4 months ago by sukesh141130 • updated 4 months ago by jrj.healey2.0k
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Venn diagram for vcf files
... Hi I used vcf-isec commands to generate common variants and unique variant files for two different plant varieties. I got vcf.gz output files. I would like to generate venn diagram for these files. I tried using vcf-isec -p option to generate the venn files. vcf-isec -p command generates files wit ...
snp written 11 months ago by sukesh141130

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

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