Moderator: Vijay Lakhujani

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Vijay Lakhujani2.8k
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India
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https://lakhujanivijay...
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vijay_lakhujani
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Last seen:
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2 years, 8 months ago
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Bioinformatician♦Programmer♦Learner


Howdy!

  • I am a bioinformatician with deep interest in Genomics, specially in next generation sequencing techniques (NGS). I enjoy programming and I usually code in Python, PERL, R and BASH. Programming is so much fun!
  • I also try to learn technical stuff with the help of MOOCs. I believe the best way to keep yourself updated is to keep learning. I also write sometimes on technical and non technical stuff. You can check out some of my articles on LinkedIn.
  • I love making new friends and discussing ideas. Do not hesitate to drop me an email if I could be of some help :)

Let's connect !

 

Posts by Vijay Lakhujani

<prev • 545 results • page 1 of 55 • next >
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Comment: C: Need help with R script to edit x-axis of snp density plot
... Hello deepti, Please use the formatting bar (especially the `code` option) to present your post better. I've done it for you this time. Thank you! ...
written 19 hours ago by Vijay Lakhujani2.8k
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Comment: C: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... For pacbio sequel data, I am running below command which fails with exit status date && time pbalign --tmpDir tmp --nproc 55 sample.fa sample.contigs.fasta out.sam Is that command fine? I am looking at [this][1] link `sample.fa`: is the pacbio sequel fastq file converted to fasta for ...
written 1 day ago by Vijay Lakhujani2.8k
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Comment: C: De novo pacBio genome assembly: How to polish data without quiver?
... Did you find anything for this? ...
written 1 day ago by Vijay Lakhujani2.8k
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Comment: C: What is the "referenceFilename" that Quiver needs to polish a assembly ?
... can you please post pbalign commands for pacbio sequel data? ...
written 1 day ago by Vijay Lakhujani2.8k
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Comment: C: Checking for a specific file type
... Are you just concerned about the file extension or do you also want your program to check the contents? ...
written 1 day ago by Vijay Lakhujani2.8k
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Comment: C: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... Hi Roxane thanks for the response. I am happy that you looked at my comment even at this point since the original post is an year old. I understand that things can change pretty quickly specially for the evolving long read sequencing. Thanks again. I am still looking through other posts and struggl ...
written 1 day ago by Vijay Lakhujani2.8k
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Comment: C: How to perform quality check and assembly using pacbio sequel data?
... Hi Harish > If you are planning to use Canu you'll need to extract the subreads > from the fastq/a file. For this you can use bam2fastq/a from smrtlink > to extract reads from bam. For that purpose, I think any general purpose bam to fastq converter will work. I used the latest version of ...
written 1 day ago by Vijay Lakhujani2.8k
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Comment: C: extract fasta sequence using fasta header with python 3
... Hello ddowlin! Questions similar to yours can already be found at: Extracting fasta sequences with identical header We have closed your question to allow us to keep similar content in the same thread. If you disagree with this please tell us why in a reply below. We'll be happy ...
written 2 days ago by Vijay Lakhujani2.8k
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Comment: C: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... I have the subreads.bam file and the assembly from canu. Can I just use the steps 1 (pbalign) and 2 (arrow) as mentioned above? Can you please point the arrow commands? ...
written 2 days ago by Vijay Lakhujani2.8k
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How to perform quality check and assembly using pacbio sequel data?
... Hi I am working with **Pacbio sequel** data for few bacterial strains. I have got 3 files from the sequencing facility - sample.bam - sample.bam.pbi - sample.subreadset.xml **Question#1** How to asses the quality of the data? Since, this is sequel data, the phred scores are arbitra ...
sequel assembly qc error correction pacbio written 3 days ago by Vijay Lakhujani2.8k

Latest awards to Vijay Lakhujani

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Popular Question 6 days ago, created a question with more than 1,000 views. For Samtools flagstat number of reads do not match actual total number of reads.
Popular Question 10 days ago, created a question with more than 1,000 views. For Samtools flagstat number of reads do not match actual total number of reads.
Popular Question 12 days ago, created a question with more than 1,000 views. For Samtools flagstat number of reads do not match actual total number of reads.
Popular Question 12 days ago, created a question with more than 1,000 views. For Error encountered while running stattest from ballgown package
Popular Question 16 days ago, created a question with more than 1,000 views. For Samtools flagstat number of reads do not match actual total number of reads.
Scholar 21 days ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Popular Question 24 days ago, created a question with more than 1,000 views. For Samtools flagstat number of reads do not match actual total number of reads.
Scholar 26 days ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Popular Question 28 days ago, created a question with more than 1,000 views. For Samtools flagstat number of reads do not match actual total number of reads.
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Error running Trinity
Scholar 5 weeks ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Appreciated 7 weeks ago, created a post with more than 5 votes. For C: bioinformatics phd .in distance education forum ...
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Samtools flagstat number of reads do not match actual total number of reads.
Great Question 7 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 7 weeks ago, created a question with more than 1,000 views. For Why does base quality of reads generally decreases at the end of the read?
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 7 weeks ago, created a question with more than 1,000 views. For Warning encountered while transcript abundance estimation using stringtie
Student 7 weeks ago, asked a question with at least 3 up-votes. For Too low mapping percentage using HISAT2 on human reference genome.
Student 8 weeks ago, asked a question with at least 3 up-votes. For Too low mapping percentage using HISAT2 on human reference genome.
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Samtools flagstat number of reads do not match actual total number of reads.
Scholar 9 weeks ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features

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