Moderator: lakhujanivijay

gravatar for lakhujanivijay
lakhujanivijay5.0k
Reputation:
4,960
Status:
Trusted
Location:
India
Website:
https://www.vijaylakhu...
Twitter:
vijay_lakhujani
Scholar ID:
Google Scholar Page
Last seen:
14 hours ago
Joined:
4 years, 6 months ago
Email:
l*************@gmail.com

Bioinformatics 💻 Programmer | Linux ❤ Lover | Constant ☕ Learner

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 !

 

Find me on ORCID

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

Posts by lakhujanivijay

<prev • 917 results • page 1 of 92 • next >
0
votes
1
answer
91
views
1
answers
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 1 day ago by lakhujanivijay5.0k
0
votes
4
answers
2.3k
views
4
answers
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 3 days ago by lakhujanivijay5.0k
0
votes
1
answer
126
views
1
answers
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 6 days ago by lakhujanivijay5.0k
0
votes
1
answer
83
views
1
answers
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 6 days ago by lakhujanivijay5.0k
0
votes
0
answers
70
views
0
answers
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 9 days ago by lakhujanivijay5.0k
0
votes
0
answers
70
views
0
answers
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 13 days ago by lakhujanivijay5.0k
0
votes
3
answers
111
views
3
answers
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 27 days ago by lakhujanivijay5.0k
0
votes
1
answer
119
views
1
answers
Answer: A: ChIA-PET2: Error: Don't have enough confident interactions to learn the model.
... Hi https://www.biostars.org/u/40156/ The best way to troubleshoot such errors is to look at the source code. The error is thrown from [these lines][1] of [this][2] R script And, this is not a new issue, someone has reported similar one [here][3]. See if you can find any clue. Sounds like it is re ...
written 4 weeks ago by lakhujanivijay5.0k
1
vote
1
answer
88
views
1
answers
Answer: A: Sum up values for a specific column of multiple files
... ``` awk -F '\t' ' {sum += $4} END {print sum}' A.txt ``` Explained [here](https://explainshell.com/explain?cmd=+awk+-F+%27%5Ct%27+%27+%7Bsum+%2B%3D+%244%7D+END+%7Bprint+sum%7D%27+A.txt#) ...
written 5 weeks ago by lakhujanivijay5.0k
2
votes
3
answers
137
views
3
answers
Answer: A: 16S-specific multiple alignment of rDNA sequences
... Di you try [PyNAST][1] ? PyNAST is pythonic implementation of [NAST][2] [1]: https://biocore.github.io/pynast/ [2]: https://academic.oup.com/nar/article/34/suppl_2/W394/2505646 ...
written 5 weeks ago by lakhujanivijay5.0k

Latest awards to lakhujanivijay

Popular Question 9 days ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Appreciated 16 days ago, created a post with more than 5 votes. For A: How to extract unmapped Paired end reads from BWA output sam file
Teacher 27 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?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Teacher 9 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?
Scholar 9 weeks 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 12 weeks 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 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?
Appreciated 3 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 4 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 4 months ago, created a question with more than 1,000 views. For How are the variants called by samtools?
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 5 months ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Popular Question 5 months ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Popular Question 5 months ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Great Question 5 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 6 months ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Scholar 6 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 6 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 6 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 7 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 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?
Student 7 months ago, asked a question with at least 3 up-votes. For What are some good resources to learn shell script for NGS pipeline development?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1027 users visited in the last hour