Moderator: lakhujanivijay

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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 )

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

Posts by lakhujanivijay

<prev • 901 results • page 1 of 91 • next >
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Answer: A: Reference of Whole exome sequecing analysis
... I prefer downloading from [iGenomes](http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/README.txt) [This](http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/Ensembl/GRCh37/Homo_sapiens_Ensembl_GRCh37.tar.gz) link should have pre-indexed genome files that you ...
written 3 days ago by lakhujanivijay4.8k
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Answer: A: FASTA file split
... Priya, you can use [seqkit][1] `seqkit split2 your_fast_file.fa -s 1000 -f` > -s, --by-size int split sequences into multi parts with N sequences [1]: https://bioinf.shenwei.me/seqkit/download/ ...
written 7 days ago by lakhujanivijay4.8k
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Answer: A: Batch rename protein fasta headers
... Using [seqkit](https://bioinf.shenwei.me/seqkit/download/) `seqkit replace -p '(.+)' -r 'one_$1' Filename.fasta` ...
written 8 days ago by lakhujanivijay4.8k
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Answer: A: Plot per base coverage from regions coverage with R
... You can use [karyoploteR][1] to achieve something like this ![enter image description here][2] [1]: https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotCoverage/PlotCoverage.html [2]: https://bernatgel.github.io/karyoploter_tutorial/Tutorial/PlotCoverage/images/Figure1-1.png **S ...
written 12 days ago by lakhujanivijay4.8k
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Comment: C: Same fastqs and pipeline get different variant results
... Use `bwa` with `-K` option with exact same value everytime ``` -K INT process INT input bases in each batch regardless of nThreads (for reproducibility) [] ``` This is well known behaviour https://www.biostars.org/p/90390/ https://www.biostars.org/p/230743/ https://www.biostars.org/p/24 ...
written 18 days ago by lakhujanivijay4.8k
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Comment: C: script to print fasta file
... And what have you tried so far? ...
written 24 days ago by lakhujanivijay4.8k
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Comment: C: Calling CNVs in exomes - CLAMMS
... Hi https://www.biostars.org/u/63728/ > Unfortunately, issues raised on GitHub are not responded yes, I have also raised several questions in the recent past and none of them were answered. So, IMHO, you should not expect any response from the author about this. I can confirm that CLAMMS does no ...
written 29 days ago by lakhujanivijay4.8k
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Comment: C: Quick way to annotate a target exome BED file with gene name information
... Thanks https://www.biostars.org/u/30/ for the edit; however, the problem remains as it is ...
written 5 weeks ago by lakhujanivijay4.8k
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Comment: C: Quick way to annotate a target exome BED file with gene name information
... What I did was 1. Downloaded GTF from Ensembl FTP ([Homo_sapiens.GRCh37.87.gtf][1]) 2. Then I made a `genes.bed` file from it awk -F "\t" '$3=="gene" {print $1 "\t" $4 "\t" $5 "\t" $9 }' Homo_sapiens.GRCh37.87.gtf | sed 's/;/\t/g' | awk -F "\t" '{print $1 "\t" $2 "\t" $3 "\t" $6}' | sed ...
written 5 weeks ago by lakhujanivijay4.8k
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Answer: C: creating chromosome plot
... Try [karyoploter][1] [1]: https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotMarkers/PlotMarkers.html ...
written 5 weeks ago by lakhujanivijay4.8k

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Teacher 11 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?
Scholar 11 days 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 4 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 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?
Appreciated 6 weeks 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 11 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?
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Popular Question 3 months ago, created a question with more than 1,000 views. For How are the variants called by samtools?
Great Question 3 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?
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
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
Teacher 5 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 5 months ago, created a question with more than 1,000 views. For How are the variants called by samtools?
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Student 5 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?
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
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