User: Vijay Lakhujani

gravatar for Vijay Lakhujani
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560
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Location:
India
Twitter:
vijay_lakhujani
Last seen:
1 week, 3 days ago
Joined:
10 months, 3 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 • 121 results • page 1 of 13 • next >
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Comment: C: Big Genome Assembly of Medicinal Plant
... I am assuming (for obvious reasons) that by "desired results", you mean the no. of scaffolds and the average scaffold size, gaps (may be!). Do you have any idea about the genome of "the" medicinal plant? Else, how are you comparing/judging your assembly? You may try using Minia or All-paths-LG. ...
written 8 weeks ago by Vijay Lakhujani560
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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 9 weeks 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 9 weeks 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 9 weeks 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 9 weeks ago by Vijay Lakhujani560 • updated 9 weeks ago by Medhat6.2k
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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 10 weeks 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 10 weeks 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 10 weeks ago by Vijay Lakhujani560 • updated 10 weeks ago by Pierre Lindenbaum91k
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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 10 weeks 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 10 weeks ago by Vijay Lakhujani560 • updated 10 weeks ago by Devon Ryan63k

Latest awards to Vijay Lakhujani

Supporter 10 weeks ago, voted at least 25 times.
Commentator 11 weeks 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 3 months ago, created 100 posts.
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Scholar 4 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 4 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Scholar 5 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 5 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Autobiographer 5 months ago, has more than 80 characters in the information field of the user's profile.
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features

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