Moderator: Vijay Lakhujani

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Vijay Lakhujani3.2k
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https://lakhujanivijay...
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vijay_lakhujani
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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 • 648 results • page 1 of 65 • next >
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Comment: C: SPAdes/QUAST how many reads contribute to a contig
... And what will that information be used for ? ...
written 2 days ago by Vijay Lakhujani3.2k
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Comment: C: nr protein db
... Hello yaghoub.amraei! Questions similar to yours can already be found at: - [Is It Possible To Extract From Ncbi Nr Database Plant Protein Sequences.?][1] 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 ...
written 2 days ago by Vijay Lakhujani3.2k • updated 2 days ago by RamRS19k
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Comment: C: Showing up and down regulated GO and pathway using enrichR and ggplot2
... https://www.biostars.org/p/309884/ ...
written 2 days ago by Vijay Lakhujani3.2k
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Comment: C: Extract a word from inside the text
... `gene.txt` is the input file. output is thrown to standard output (stdout) ...
written 2 days ago by Vijay Lakhujani3.2k
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Comment: C: how to create a gff3 file of gap regions in an assembly?
... Dear https://www.biostars.org/u/26550/ Sure, give it a try ! If this is helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. ![Upvote|Bookmark|Accept][1] [1]: http://i68.tinypic.com/2m2ykjr.png ...
written 2 days ago by Vijay Lakhujani3.2k
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Answer: A: Extract a word from inside the text
... Super fast and easy using `grep` pattern matching using regex grep -P '(?<=\*\*gene=)\w+(?=\*\*)' -o gene.txt where `gene.txt` if your file name **Output** NECTIN3 TAGLN3 SMG6 ERICH1 DLGAP2 PPP2R2B **Explanation** `-P` Means pattern `?<=` Left Anchor `? ...
written 3 days ago by Vijay Lakhujani3.2k
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Answer: A: how to create a gff3 file of gap regions in an assembly?
... Ultrafast solution **toy fasta file** $ cat fasta.fa >1 TGTACGTNNATT >2 TTTAANNTTTNN >3 NNTT TTNN **solution using [seqkit][1]** seqkit locate -p N+ fasta.fa --gtf -P **output** 1 SeqKit location 8 9 0 + . gene_id "N+"; 2 SeqKit location 6 ...
written 3 days ago by Vijay Lakhujani3.2k
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Comment: C: How to convert chrM variants from NC_001807.4 version coordinates to NC_012920.1
... Hi https://www.biostars.org/u/40156/ That's appears to be difficult because RefSeq NC_001807 is an African (Yoruban) sequence with over 40 variant nucleotides from the rCRS. On July 8, 2009 the sequence [was removed from GenBank][1] as a reference sequence but may be found. The rCRS has a new numbe ...
written 4 days ago by Vijay Lakhujani3.2k
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Answer: A: Errors with samtools depth on merged bam file
... "EOF marker is absent" refers to the absence of a special empty BGZF block of 28 bytes, which samtools looks for at the end of the data to indicate the BAM file is complete. **If you see that error, either:** (a) Your file is somehow truncated or incomplete (Chances are more that this is the issue ...
written 4 days ago by Vijay Lakhujani3.2k
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Comment: C: What would be the trend in next few years in NGS era?
... A similar post https://www.biostars.org/p/257336/ ...
written 5 days ago by Vijay Lakhujani3.2k

Latest awards to Vijay Lakhujani

Teacher 11 hours ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Popular Question 7 days ago, created a question with more than 1,000 views. For What are some good resources to learn shell script for NGS pipeline development?
Popular Question 17 days ago, created a question with more than 1,000 views. For What are some good resources to learn shell script for NGS pipeline development?
Popular Question 18 days ago, created a question with more than 1,000 views. For What are some good resources to learn shell script for NGS pipeline development?
Popular Question 18 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?
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Popular Question 22 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 5 weeks ago, created a question with more than 1,000 views. For Error encountered while running stattest from ballgown package
Commentator 9 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 3 months ago, created a question with more than 1,000 views. For Too low mapping percentage using HISAT2 on human reference genome.
Popular Question 3 months ago, created a question with more than 1,000 views. For Error encountered while running stattest from ballgown package
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For C: bioinformatics phd .in distance education forum ...
Appreciated 3 months ago, created a post with more than 5 votes. For C: bioinformatics phd .in distance education forum ...
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Draw circular genome with selected features
Popular Question 4 months 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 4 months 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 4 months ago, created a question with more than 1,000 views. For Error encountered while running stattest from ballgown package
Popular Question 4 months 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 4 months 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 4 months ago, created an answer that has been accepted. For A: Just complement or reverse sequence fom Biopython, but not reverse-complement on
Popular Question 4 months ago, created a question with more than 1,000 views. For Samtools flagstat number of reads do not match actual total number of reads.

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