Moderator: lakhujanivijay

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lakhujanivijay4.7k
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Bioinformatics 💻 Programmer | Linux ❤ Lover | Constant ☕ Learner

A passionate bioinformatician interested in developing solutions for analyzing, visualizing and integrating clinical and research data.

Me = ( ¼ Bioinformatician ) + ( ¼ Programmer ) +  ( ½ Biologist )

Let's connect !

 

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ORCID iD iconhttps://orcid.org/0000-0002-6529-0841

Posts by lakhujanivijay

<prev • 890 results • page 1 of 89 • next >
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Comment: C: How to create a Fasta file using info from a Excel file
... What have you tried so far? Please do not expect ready made answers. ...
written 2 days ago by lakhujanivijay4.7k
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Comment: C: converting taxID to taxonomy
... Did you try [taxonkit][1] [1]: https://bioinf.shenwei.me/taxonkit/usage/ ...
written 3 days ago by lakhujanivijay4.7k
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Comment: C: How to integrate custom variant callers for consensus genotyping using CGES?
... https://www.biostars.org/u/41746/ I did not get you. ...
written 4 weeks ago by lakhujanivijay4.7k
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How to integrate custom variant callers for consensus genotyping using CGES?
... Hi All I am interested in calling consensus genotype for few germline samples using BAM files as initial inputs. The CGES (Consensus Genotyper for Exome Sequencing) [paper][1] describes a workflow where they have integrated 4 different variant callers - GATK, samtools, FreeBayes and Atlas-SNP-2. W ...
genotyping cges consens variant germline written 4 weeks ago by lakhujanivijay4.7k
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Comment: C: How to assemble contigs?
... Thanks for sharing this information https://www.biostars.org/u/30/ ...
written 4 weeks ago by lakhujanivijay4.7k
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Comment: C: Is there any way to download knownCanonical set from the NCBI Refseq track as it
... I am trying to run DepthOfCoverage from GATK3 (it's an old - no more supported version) which requires RefSeq file , however, that files contains all transcripts and not just canonical transcript. I was wondering how can I generate that file. ...
written 6 weeks ago by lakhujanivijay4.7k
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Is there any way to download knownCanonical set from the NCBI Refseq track as it is possible for the UCSC track ?
... From the UCSC genome browser, is there any way to download *knownCanonical* set from the **NCBI Refseq** track as it is possible for the **UCSC** track (see screenshot below) *knownCanonical* is not available in the dropdown in **table** option when we select **NCBI Refseq** ...
table browser ucsc canonical refseq hg19 written 6 weeks ago by lakhujanivijay4.7k • updated 4 weeks ago by jnavarr510
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Answer: A: What do you think of sci-hub?
... Looks like almost everyone across the world us using scihub Source : [Who's downloading pirated papers? Everyone][1] [1]: https://www.sciencemag.org/news/2016/04/whos-downloading-pirated-papers-everyone ...
written 7 weeks ago by lakhujanivijay4.7k
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Comment: C: how to use output of cnvkit to plot
... You can try [CopyNumberPlots][1] [1]: http://www.bioconductor.org/packages/devel/bioc/vignettes/CopyNumberPlots/inst/doc/CopyNumberPlots.html ...
written 7 weeks ago by lakhujanivijay4.7k
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Comment: C: to calculate coverage of each contig after assembly
... Hi Jyotika, > [1] I have the read file and assembled contigs (both in .fasta format) Reads in fasta? Are you sure its not fastq rather? > [2] I need to calculate the coverage for each single contigs across the read file This does not make sense . What do you mean by *across the read file*? ...
written 8 weeks ago by lakhujanivijay4.7k

Latest awards to lakhujanivijay

Appreciated 3 days ago, created a post with more than 5 votes. For A: How to extract unmapped Paired end reads from BWA output sam file
Great Question 5 weeks ago, created a question with more than 5,000 views. For How to install samtools v.1.2 on Ubuntu 14.0 32 bit?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For How to install samtools v.1.2 on Ubuntu 14.0 32 bit?
Popular Question 8 weeks ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Popular Question 8 weeks ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Great Question 9 weeks ago, created a question with more than 5,000 views. For How to install samtools v.1.2 on Ubuntu 14.0 32 bit?
Popular Question 12 weeks ago, created a question with more than 1,000 views. For How are the variants called by samtools?
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: How to apply a function to a list and get results as a list in R?
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: How to apply a function to a list and get results as a list in R?
Popular Question 4 months ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Popular Question 4 months ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Student 4 months ago, asked a question with at least 3 up-votes. For What are some good resources to learn shell script for NGS pipeline development?
Appreciated 4 months ago, created a post with more than 5 votes. For A: How to extract unmapped Paired end reads from BWA output sam file
Student 5 months ago, asked a question with at least 3 up-votes. For What are some good resources to learn shell script for NGS pipeline development?
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
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For C: bioinformatics phd .in distance education forum ...
Popular Question 7 months ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Popular Question 7 months ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Popular Question 8 months ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Popular Question 8 months ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Scholar 8 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

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