User: Vijay Lakhujani

gravatar for Vijay Lakhujani
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560
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India
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vijay_lakhujani
Last seen:
1 day, 14 hours ago
Joined:
8 months, 2 weeks ago
Email:
l*************@gmail.com

☛     Genomics Domain Specialization: NET-JRF, GATE, BINC qualified.

☛     Certified bioinformatician (by Dept. of Biotechnology, Govt. of India), All India Rank 18, BINC 2012).

☛      5+ years of experience in Genomics service based industry in India including 3.5+ years of experience in next generation sequencing data analysis.

☛     Skilled in working with commercial/open source software for microarray and NGS end-to-end data analysis, from raw sequencing data to variant reporting. Whole genome,transcriptome, 16S rRNA NGS data analysis, de novo assembly tools & algorithms, assembly validation and downstream data processing.

☛     Sound knowledge of open source tools for data visualization and interpretation. Comfortable with working on Linux platform & HPC.

Posts by Vijay Lakhujani

<prev • 120 results • page 1 of 12 • next >
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Comment: C: Error executing bedops convert2bed
... Thank you the information on the difference of both. By any means, can I allocate more memory OR assign more number of threads? Due to confidential nature of the data, I will not be able to share the same. What I can tell you at this point is that the file has been created using GATK (HaplotypeCalle ...
written 5 days ago by Vijay Lakhujani560
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Error executing bedops convert2bed
... **Objective: to convert vcf to bed** **Tool used: [bedops][1]** **Command:** /home/bedops/bin/convert2bed -i vcf < my.vcf > my.bed **Error encountered** Error: Could not allocate space for VCF INFO string [1]: http://bedops.readthedocs.io/en/latest/index.html ***QUESTIONS:** ...
vcf bed bedops convert2bed written 5 days ago by Vijay Lakhujani560
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Comment: C: What is the best method to map snps called using GATK to corresponding genes?
... Thanks, I downloaded and checked the database for the presence of my genome of interest (i am looking for sesame indicum) without luck! From a first look at the file, it seems it only supports bacterial genomes. Any further suggestions? ...
written 5 days ago by Vijay Lakhujani560
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What is the best method to map snps called using GATK to corresponding genes?
... Hi, I have a list of snp's in a vcf file called using `GATK` for a plant genome. Now, the objective is to map those SNP's to corresponding genes in the genome (I have the reference genome and corresponding GFF file with me) since I have the SNP positions in the `POS` column of vcf along with the ch ...
gene gatk snp written 6 days ago by Vijay Lakhujani560 • updated 6 days ago by Medhat6.0k
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Comment: C: Filtering out the variants annotated as "FILTER" from vcf file using GATK
... Uh oh. I just checked the vcf and found that I don't have any ID's in the vcf i.e. the 3rd column just contains a dot for each and every row. Apparently, I missed a step which assigns ID's to the variants? Any clues? ...
written 6 days ago by Vijay Lakhujani560
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Comment: C: Filtering out the variants annotated as "FILTER" from vcf file using GATK
... Thanks [WouterDeCoster][1] for the prompt response. Just to be sure, here `ID` would be the 3rd column in the vcf file, right? #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sesamum_Indicum.L [1]: https://www.biostars.org/u/24526/ ...
written 6 days ago by Vijay Lakhujani560
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Filtering out the variants annotated as "FILTER" from vcf file using GATK
... Hi, I am using GATK to filter out variants (specifically SNP's) based on mapping quality For tagging the variants which failed the MQ(mapping quality) filter, I ran the following commands from GATK java -Xmx10g -jar /state/partition1/results/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T Varia ...
vcf gatk snp filter written 6 days ago by Vijay Lakhujani560 • updated 6 days ago by Pierre Lindenbaum88k
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Comment: C: Weird issue with bam file generated by samtools
... 1. Ah! silly mistake!! Thanks for pointing that! 2. Upgrading samtools . . . ...
written 12 days ago by Vijay Lakhujani560
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Weird issue with bam file generated by samtools
... I generated a bam file following the below steps: **indexed reference genome** bwa index reference.fasta **aligned using bwa mem** bwa mem ref.fasta f1.fq.gz f2.fq.gz > out.sam **sam to bam** samtools view -Sb out.sam > out.bam **sorting bam** samtools sort out.ba ...
samtools bam bwa mem written 12 days ago by Vijay Lakhujani560 • updated 12 days ago by Devon Ryan60k
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Answer: A: 16S rRNA seq software
... I would strongly suggest using QIIME Start here: a. http://www.wernerlab.org/teaching/qiime [Tutorial with explanation] b. [Youtube videos - extensive explanation] https://www.youtube.com/watch?v=6564K4-_DBI c. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249058/ [Research paper] QIIME Ho ...
written 12 days ago by Vijay Lakhujani560

Latest awards to Vijay Lakhujani

Supporter 12 days ago, voted at least 25 times.
Commentator 18 days ago, created a comment with at least 3 up-votes. For C: how to extract particular regions of a sequence from fasta file if its range fo
Centurion 27 days ago, created 100 posts.
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Scholar 8 weeks ago, created an answer that has been accepted. For A: How do i should proceed with 16S rRNA amplicon sequencing data from Illumina MiS
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Scholar 3 months ago, created an answer that has been accepted. For A: How do i should proceed with 16S rRNA amplicon sequencing data from Illumina MiS
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Autobiographer 3 months ago, has more than 80 characters in the information field of the user's profile.
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features

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