Moderator: lakhujanivijay

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lakhujanivijay5.1k
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Bioinformatician 💻 | ☕  Programmer 

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 • 920 results • page 1 of 92 • next >
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Comment: C: ACMG 59 genes
... see [this][1] article [1]: https://www.nature.com/articles/s41436-019-0502-5 ...
written 25 days ago by lakhujanivijay5.1k
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Comment: C: SAVE biostars.org from FAKE and unnecesary answers
... > This website is full of maximum unnecessary answers I don't agree with this. Biostars has been the most accessed and valued resource for bioinformatics. > few people ask questions instead of providing any clues Asking questions is important most of the times in scenarios when: 1. The que ...
written 4 weeks ago by lakhujanivijay5.1k
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Comment: C: Get summary of aligned sequences
... I believe what https://www.biostars.org/u/1767/ meant is to perform clustering of the protein sequences first; i.e. cluster similar protein sequences into clusters that meet a user-defined similarity threshold. This could be achieved using clustering tools such as CD-HIT; have a look [this](http://w ...
written 4 weeks ago by lakhujanivijay5.1k
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Answer: A: How to call and INDEL using GATK
... Hi https://www.biostars.org/u/17505/ That's a header incompatibility issue and can be resolved by editing your reference fasta file. Here are few suggestions: 1. check the headers of your reference fasta file: `grep "^>" /home/kumarm/allan-work/RNASEq-alignment/ref_sequence.fa` 2. check the ...
written 9 weeks ago by lakhujanivijay5.1k
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4
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Answer: A: fastq to fasta perl
... See a [python script][1] which I wrote sometimes back [1]: https://raw.githubusercontent.com/lakhujanivijay/Bioinformatics-Problems-Rosalind/master/FastQ_to_fasta_converter/fastq_2_fasta.py ...
written 10 weeks ago by lakhujanivijay5.1k
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Answer: A: Calling CNVs in exomes - CLAMMS
... The supplementary information [here][1] says > Query our laboratory information management system to retrieve seven > Picard sequencing quality control metrics for each sample: GCDROPOUT, > ATDROPOUT, MEANINSERTSIZE, ONBAITVSSELECTED, PCTPFUQREADS, > PCTTARGETBASES10X, and PCTTARGETBASE ...
written 10 weeks ago by lakhujanivijay5.1k
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Comment: C: Biopython vs Python
... If you need to work with the biopython package, you need that. Think it this way, if you have windows OS, do you need microsoft office ? Answer is yes, if you need powerpoint! ...
written 10 weeks ago by lakhujanivijay5.1k
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149
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Comment: C: Installing gatk inside singularity container
... Thanks https://www.biostars.org/u/18713/ However I am attempting an installation from the scratch, reason being installing a big set of tools (along with GATK). ...
written 11 weeks ago by lakhujanivijay5.1k
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149
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Installing gatk inside singularity container
... Hi everyone, I am wondering whether anyone tried installing GATK inside a singularity container. I can see that there is a tutorial on how to install [gatk inside a docker container][1], however, I could not find anything about singularity. My current approach is to install conda inside my contain ...
gatk singularity container written 11 weeks ago by lakhujanivijay5.1k
0
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164
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Answer: A: How to add file name after > in a multi-fasta file?
... using [seqkit][1] `seqkit replace -p '(.+)' -r '${1}_HTH_7' sample_1.fasta` [1]: https://bioinf.shenwei.me/seqkit/download/ ...
written 3 months ago by lakhujanivijay5.1k

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Popular Question 13 days 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 23 days ago, created a question with more than 1,000 views. For How to install samtools v.1.2 on Ubuntu 14.0 32 bit?
Commentator 25 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
Popular Question 4 weeks ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Appreciated 4 weeks ago, created a post with more than 5 votes. For A: How to extract unmapped Paired end reads from BWA output sam file
Commentator 4 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
Popular Question 6 weeks ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For How are the variants called by samtools?
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Appreciated 12 weeks ago, created a post with more than 5 votes. For A: How to extract unmapped Paired end reads from BWA output sam file
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 3 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?
Teacher 4 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 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
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: How to apply a function to a list and get results as a list in R?
Appreciated 5 months 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 6 months 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 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 to install samtools v.1.2 on Ubuntu 14.0 32 bit?
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 7 months ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Great Question 7 months ago, created a question with more than 5,000 views. For How to install samtools v.1.2 on Ubuntu 14.0 32 bit?

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