User: sukesh1411

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sukesh141130
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Location:
South Africa
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11 hours ago
Joined:
1 year, 9 months ago
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s*********@gmail.com

Posts by sukesh1411

<prev • 44 results • page 1 of 5 • next >
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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 5 days 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 5 days ago by sukesh141130 • updated 4 days ago by jrj.healey1.2k
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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 7 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 7 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 7 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 7 months ago by sukesh141130 • updated 4 days ago by Biostar ♦♦ 10
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Comment: C: Aligning two genomes in fastq.gz
... Its related to japonica and i will do variant calling against it. Thank you sir. ...
written 7 months ago by sukesh141130
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Comment: C: Known SNPs for rice for Base recalibration using GATK
... Hi Am also working on rice genome. Can i use snps from the below database to perform base recalibration? http://www.oryzasnp.org/_download.zul/Nipponbare ...
written 7 months ago by sukesh141130
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Comment: C: Aligning two genomes in fastq.gz
... Thank you sir. I am working on two different varieties of oryza sativa. ...
written 7 months ago by sukesh141130
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Aligning two genomes in fastq.gz
... Hi I would like to find the variants among two different genomes (both are paired end reads). I removed the low quality reads for two genomes using sickle tool. Now i got two paired end output files from sickle which are in fastq.gz format. Can anyone suggest me the tool for aligningtwo different ...
bwa written 7 months ago by sukesh141130 • updated 7 months ago by Chris Cole620

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Popular Question 4 months ago, created a question with more than 1,000 views. For convert text file to fasta file

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