Moderator: lakhujanivijay

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lakhujanivijay5.3k
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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 )

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

Posts by lakhujanivijay

<prev • 932 results • page 1 of 94 • next >
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Is there any tool/API available to convert GTF/GFF to JSON format?
... Hi all Before I start writing my own code to convert GTF file into a JSON format file, has anyone came across any API or tool to either convert or download the file is JSON ? I am looking for a format like this - `gene -> transcript -> exon` : "MOS": { "NM_005372.1": [ ...
gtf ncbi gff json ensembl written 5 weeks ago by lakhujanivijay5.3k • updated 5 weeks ago by vkkodali2.4k
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Comment: C: how to choose hub genes in wgcna
... Hi Parin Check out similar posts on Biostars and see if that helps https://www.biostars.org/p/419867/ https://www.biostars.org/p/294436/ Similar posts appear on the right of the original post ...
written 12 weeks ago by lakhujanivijay5.3k
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Comment: C: error while executing panX script (KeyError: 'db_xref').
... The program specific issues are hard to resolve here because many of the tools are not that popular. Best option is to raise an issue of the respective github repository. I could see similar issue reported [here][1] with no solution [1]: https://github.com/neherlab/pan-genome-analysis/issues/36 ...
written 3 months ago by lakhujanivijay5.3k
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Comment: C: Help needed with LOHHLA pipeline
... https://www.biostars.org/u/49081/ were you able to resolve the issue ? Can you check once if your BAM file is not truncated ? \* `samtools quickcheck -v -v -v -v ` \* Requires latest samtools version ...
written 3 months ago by lakhujanivijay5.3k
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Comment: C: network construction in cytoscape
... Hi https://www.biostars.org/u/63328/ Can you point us to the tutorial you are following ? ...
written 3 months ago by lakhujanivijay5.3k
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Answer: A: phenotype in meta analysis
... Hi Parin Quoting from [this][1] paper > One approach to increase power for GWASs on a phenotype that is hard > to collect is to utilize an intermediate or proxy phenotype that is > correlated to the target phenotype of interest. In this approach, one > intermediate or proxy phenotype, ...
written 3 months ago by lakhujanivijay5.3k
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Comment: C: Chia-pipe cannot find the module pigz
... Hi https://www.biostars.org/u/40156/ `/WGS_tools/ChIA-PIPE/0.chia_pipe_shell.sh: line 208: pigz: command not found` I could also see this error in your original post; were you able to resolve this? ...
written 4 months ago by lakhujanivijay5.3k
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Comment: C: Variant Calling pipeline to be run parallel on multiple cores
... Agree with what https://www.biostars.org/u/30/ said ...
written 4 months ago by lakhujanivijay5.3k
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Comment: C: Variant Calling pipeline to be run parallel on multiple cores
... **Using [GNU parallel][1] instead** > **psuedo code** import subprocess cmd_file_name = cmd_file.txt cmd_file = open(cmd_file_name, "a") jobs = 20 for i in your_sample_list : cmd = " ".join( [ "your command", "-i" , i ] ) cmd_file.write(cmd, "\n ...
written 4 months ago by lakhujanivijay5.3k • updated 4 months ago by _r_am32k
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Comment: C: hhblits and pssm
... Hi https://www.biostars.org/u/67543/ The title "hhblits and pssm" does not qualify as a good/informative title to your post. Please elaborate the title. ...
written 4 months ago by lakhujanivijay5.3k

Latest awards to lakhujanivijay

Teacher 28 days 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?
Teacher 5 weeks 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 7 weeks ago, created a question with more than 1,000 views. For What are some good platforms to exhibit bioinformatics skills online?
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?
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Popular Question 12 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 3 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?
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
Popular Question 3 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?
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
Popular Question 3 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 3 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?
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
Popular Question 5 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 6 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 6 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?
Commentator 6 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
Popular Question 6 months ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Appreciated 6 months ago, created a post with more than 5 votes. For A: How to extract unmapped Paired end reads from BWA output sam file
Commentator 6 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
Popular Question 6 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?

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