User: Vijay Lakhujani

gravatar for Vijay Lakhujani
Reputation:
560
Status:
Trusted
Location:
India
Twitter:
vijay_lakhujani
Last seen:
2 hours ago
Joined:
11 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 (specially NGS 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 • 136 results • page 1 of 14 • next >
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Comment: C: What is DeNovo Assembly?
... You could google next time before asking. ...
written 4 days ago by Vijay Lakhujani560
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Merging stringtie assemblies using stringtie merge
... I have a set of 2 transcriptome samples **Sample1 - A. control B. treated** **Sample2 - A. control B. treated** I assembled the transcriptome using stringtie **Objective is to compare A vs B for sample1 and A vs B for sample2.** How should I merge the assemblies using `stringtie --merge` ? Sho ...
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Comment: C: Warning encountered while transcript abundance estimation using stringtie
... Looking at the code [here][1], the error is seen when: if (guided && no_ref_used) { GMessage("WARNING: no reference transcripts were found for the genomic sequences where reads were mapped!\n" "Please make sure the -G annotation file uses the same naming convention f ...
written 7 days ago by Vijay Lakhujani560
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Comment: C: The problem using samtools stats
... What is the command that you are running? Also, please share it's output. ...
written 7 days ago by Vijay Lakhujani560
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Comment: C: Warning encountered while transcript abundance estimation using stringtie
... Should I then give it a try by removing the ":" ? Or the whole thing along with the colon sign? ...
written 7 days ago by Vijay Lakhujani560
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Comment: C: Warning encountered while transcript abundance estimation using stringtie
... Yes, absolutely! I confirmed the same by fetching the sequence from the reference fasta file from the gf file using `bedtools getfasta` ...
written 7 days ago by Vijay Lakhujani560
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Comment: C: Warning encountered while transcript abundance estimation using stringtie
... **"transcript"** #!genome-build-accession GCA_000003745.2 1 Genoscope chromosome 1 23037639 . . . ID=chromosome:1;Alias=FN597015.1 ### 1 iggp gene 10731 27597 . + . ID=gene:VIT_01s0011g00010;biotype=pr ...
written 7 days ago by Vijay Lakhujani560
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Comment: C: Warning encountered while transcript abundance estimation using stringtie
... > Have you checked your gff3 file looks valid? gffread -E reference.gff3 GFF: discarding unrecognized feature "chromosome" ID=chromosome:1 GFF: discarding unrecognized feature "chromosome" ID=chromosome:10 GFF: discarding unrecognized feature "chromosome" ID=chromosome:10_random ...
written 8 days ago by Vijay Lakhujani560
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Warning encountered while transcript abundance estimation using stringtie
... I am trying to run stringtie for transcript abundance estimation using below command: for i in *.sorted.bam; do sample_name=`echo $i| awk -F "." '{print $1}'`; stringtie -e -B -p 60 -G stringtie-merged.gtf -o $sample_name.gtf $i;done **Warning encountered:** > WARNING: no reference transcri ...
stringtie rna-seq abundance written 8 days ago by Vijay Lakhujani560
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Answer: A: How to systematically check if a bam file is truncated
... A truncated bam file will **NOT** produce this result when provided as an input to `file` command: >file your.bam your.bam: gzip compressed data, extra field ...
written 8 days ago by Vijay Lakhujani560

Latest awards to Vijay Lakhujani

Supporter 3 months ago, voted at least 25 times.
Commentator 3 months 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 4 months ago, created 100 posts.
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
Scholar 6 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 6 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Autobiographer 7 months ago, has more than 80 characters in the information field of the user's profile.
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features

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