User: sukesh1411

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sukesh141130
Reputation:
30
Status:
New User
Location:
South Africa
Last seen:
1 week, 1 day ago
Joined:
1 year, 11 months ago
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Posts by sukesh1411

<prev • 48 results • page 1 of 5 • next >
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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 10 days 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 10 days 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 days 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 4 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 9 weeks 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 9 weeks ago by sukesh141130 • updated 9 weeks ago by jrj.healey1.6k
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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 9 months ago by sukesh141130
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Comment: C: Realigner Target Creator
... thank you sir. i will try in latest version of GATK. ...
written 9 months ago by sukesh141130
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Comment: C: Realigner Target Creator
... Hi Thank you sir. Again the same error if i use the --known. As i said i tried -known, -- known --variants. Will the version of tool matters? Thanks ...
written 9 months ago by sukesh141130
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Realigner Target Creator
... Hi I am currently using GATK-1.0 version to run the RealignerTargetCreator to perform local realignment around indels. command: java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R ../../rice/IRGSP-1.0_genome.fasta -I uniqueKAVUNI1.bam -known oryza_sativa.vcf -o target_intervals.list. I ...
software error written 9 months ago by sukesh141130 • updated 9 weeks ago by Biostar ♦♦ 20

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

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