User: Vijay Lakhujani

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Vijay Lakhujani2.1k
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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 • 402 results • page 1 of 41 • next >
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Comment: C: I get almost the same fastqc report for a fastq file before and after using Trim
... Strange that it worked for you without specifying quality `INT` in `-q` option. It failed in my case /opt/app/TrimGalore-0.4.5/trim_galore --fastqc --illumina ../test.fq -q Option q requires an argument Please respecify command line options I checked the help /opt/app/TrimGalore-0 ...
written 1 minute ago by Vijay Lakhujani2.1k
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Answer: A: about the alignement
... This appears to me as the most trivial nucleotide identity matrix, however, please format it correctly. Generally, `1` being match and `0` being mismatch. In a diagonally symmetric matrix like this , the order of the nucleotide in the rows and columns should be same. ...
written 21 hours ago by Vijay Lakhujani2.1k
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Comment: C: plot the distribution
... Please provide headers to your columns for others to understand ...
written 21 hours ago by Vijay Lakhujani2.1k
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Answer: A: How do you use BLAST?
... I have frequently used **BLAT** for aligning microarray probes (expression array probes ; generally ~60 bp, Agilent). Most of the times, the objective was to identify the gene it originated from or for the annotation. ...
written 3 days ago by Vijay Lakhujani2.1k
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Answer: A: Plink sex check - why would female calls have more than 0 nonmissing Y genotypes
... I don't know much about GWAS but I can surely give a analogy from microarray experiments. Sometimes, you may see aberrations in the Y chromosome in case of CGH arrays despite the sample being female. There is a concept of unique and non-unique probes. The unique probes have the same chromosome numb ...
written 4 days ago by Vijay Lakhujani2.1k • updated 3 days ago by zx87544.3k
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Comment: C: karyoploteR: uncircle your genomes
... Can you just briefly tell me the steps; I will figure out the exact commands myself. What I have is - a genome file in fasta format (chr wise) - a corresponding GTF file - a read count file gene wise as shown above ...
written 4 days ago by Vijay Lakhujani2.1k
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Answer: A: Combining different tasks in one line of code in terminal
... Of course, if you want to do with your data being in the excel format and that too programatically (sensibly; **synonym** :D ) then may be you can use file parsers designed specially to manipulate excel files for e.g. [this][1] one. Next option is transforming all data into simple text files and m ...
written 4 days ago by Vijay Lakhujani2.1k
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Answer: A: karyoploteR: uncircle your genomes
... Hi Very nice project. I am wondering if i could draw a barplot on a custom genome depicting the reads mapped on particular features; say "genes". So, that will be a pretty simple data set as given below GeneID RawReadCount 14490.2 5 011470.2 24 14480.1 0 025190.2 12 ...
written 4 days ago by Vijay Lakhujani2.1k
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Comment: C: Hisat2 alignment error
... Could you try changing this --novel-splicesite-outfile /data/memona/hisat2-2.1.0/result/ to --novel-splicesite-outfile /data/memona/hisat2-2.1.0/result/novel.sites.txt ...
written 4 days ago by Vijay Lakhujani2.1k
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Answer: A: Hisat2 alignment error
... Looks like these issues have been already taken care in the recent version. Check your HISAT version using hisat2 --version Update if necessary ...
written 4 days ago by Vijay Lakhujani2.1k

Latest awards to Vijay Lakhujani

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
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.
Scholar 8 weeks ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Popular Question 12 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 12 weeks ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Scholar 5 months ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Voter 5 months ago, voted more than 100 times.
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Scholar 7 months ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Scholar 8 months ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Scholar 9 months ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Scholar 10 months ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Scholar 10 months ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Guru 10 months ago, received more than 100 upvotes.
Scholar 11 months ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Scholar 11 months ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Scholar 12 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 12 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features

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