User: Samarth Kulshrestha

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180
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India
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https://samarthkulshre...
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1 year, 5 months ago
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5 years, 7 months ago
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Bioinformatician by profession and experience in building, managing high-throughput data and analysis pipelines for processing of data generated from massively parallel sequencing platforms (Illumina 2000/2500) for DNA sequencing. Currently an active member of ICGC India project. My work of interest is Cancer genomics using Next Generation Sequencing Data Analysis.

https://www.slideshare.net/SamarthKulshrestha

 

 

Posts by Samarth Kulshrestha

<prev • 33 results • page 1 of 4 • next >
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Comment: A: CNV detection using beakdancer and SVDetect
... Hi Mahsa, Can you please provide more details about the output generated by those SV callers? Generally these callers reports different types of Structural Variants (SV) sites in the genome. There are variety of CNV callers are available for CNV detection,you can look for [Control-FREEC][1], [BICs ...
written 18 months ago by Samarth Kulshrestha180
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Comment: C: Split BAM file.
... Hi, As recommended by Cameron, you should also provide the details of the error message you gets during your process. You can look for this SAM to BAM conversion command, I believe that your bowtie2 process is generating SAM file in proper format. The command mentioned below should generate a pro ...
written 18 months ago by Samarth Kulshrestha180 • updated 8 weeks ago by RamRS21k
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Answer: A: Split BAM file.
... Hi, You can also explore BamTools toolkit with **"split"** option. usage: bamtools [--help] COMMAND [ARGS] Available bamtools commands: convert Converts between BAM and a number of other formats count Prints number of alignments in BAM file(s) coverage ...
written 18 months ago by Samarth Kulshrestha180
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Answer: A: GISTIC-segmentation overlaps error
... Hi, Can you paste the input data (few lines) which you are using as INPUT for GISTIC program? I would like to check the data structure to understand the problem. Thanks ...
written 19 months ago by Samarth Kulshrestha180
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Answer: A: How to use samtools/bcftoos/vcfutils to call SNP
... Hi, You can follow the instructions on the given link : [http://samtools.sourceforge.net/mpileup.shtml][1] Well explained with all the commands for SNP/INDEL calling using SAMtools. Best [1]: http://samtools.sourceforge.net/mpileup.shtml ...
written 19 months ago by Samarth Kulshrestha180
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Answer: A: SAMtools installation on windows
... Hi, You might be interested in knowing that **Windows 10 offers a new feature, A full, Ubuntu-based Bash shell that can run Linux software directly on Windows**. [https://msdn.microsoft.com/en-us/commandline/wsl/about][1] [https://www.howtogeek.com/265900/everything-you-can-do-with-windows-10s-n ...
written 19 months ago by Samarth Kulshrestha180
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Comment: C: Detecting Structural variants in sequencing data
... There are plenty of SV callers available which use sequencing data. You need to be specific about your SV types, Somatic or Germline. You can always realign your fastq reads using a different aligner. [Breakdancer][1], [Lumpy][2], [Delly][3], [SVdetect][4], [Pindel][5] are some of popular SV caller ...
written 19 months ago by Samarth Kulshrestha180
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Comment: C: Difference between genomes in circular graph
... You can use [CIRCOS][1], one of the popular visualization tool, written in PERL as suggested by Pierre. There is one more R package which can help you ie.[CIRCUS][2]. [1]: http://genome.cshlp.org/content/19/9/1639.full [2]: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-21 ...
written 19 months ago by Samarth Kulshrestha180
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Comment: C: Circos image for Copy Number Variation
... Hi, There are number of published study where CNV tracks have been plotted in a circular fashion using CIRCOS. I strongly suggest you to explore more of genomics research article for your reference. Below is a link of article [for your reference] where authors have generated a CNV frequency plot. I ...
written 19 months ago by Samarth Kulshrestha180
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Answer: A: Circos image for Copy Number Variation
... Hi, There are different ways of representing data in a circular format (CIRCOS). http://circos.ca/documentation/tutorials/recipes/copy_number_data/lesson Go through the link mentioned above, here is one of the tutorials you can plot your CNV values with circos. Best ...
written 19 months ago by Samarth Kulshrestha180

Latest awards to Samarth Kulshrestha

Popular Question 18 months ago, created a question with more than 1,000 views. For PatternCNV : tool detects DNA copy number of variations
Scholar 19 months ago, created an answer that has been accepted. For A: Extracting coverage per base pair
Scholar 20 months ago, created an answer that has been accepted. For A: Extracting coverage per base pair
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Germline CNV caller
Popular Question 5.0 years ago, created a question with more than 1,000 views. For How To Find Reads With Secondary Alignment In Bwa Mem Sam File ?
Autobiographer 5.2 years ago, has more than 80 characters in the information field of the user's profile.

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