User: Samarth Kulshrestha

Reputation:
200
Status:
Trusted
Location:
India
Website:
https://samarthkulshre...
Last seen:
1 year, 11 months ago
Joined:
6 years ago
Email:
s********@gmail.com

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 2 of 4 • next >
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Comment: C: how to read indexed bamfiles
... Correctly said by Chris, Input requirement for **samtools depth** is .bam file not .bai (indexed) file **samtools depth -r ** .bam Above command should work. (Also make sure that **.bam** and **.bai** are in the same directory) ...
written 2.1 years ago by Samarth Kulshrestha200
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Comment: C: regarding Break dancer ouput
... What i can see here, In the Library statistics section of DK_sort.bam: DK_sort.bam mean:1021.13 std:300.81 uppercutoff:2543.75 lowercutoff:214.78 readlen:145.58 library:7 reflen:518514126 **seqcov:0 phycov:0** Both coverage parameter, seq coverage (seqcov) and physical coverage ( ...
written 2.1 years ago by Samarth Kulshrestha200
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Answer: A: regarding Break dancer ouput
... Deepika, Breakdancer Output is well explained here (check the link): https://github.com/kenchen/breakdancer Hope this helps ...
written 2.1 years ago by Samarth Kulshrestha200
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Answer: A: Can anyone suggest a good tutorial to learn RNA-seq analysis?
... Hello, You can follow the blog "RNAseq Blog", an informative blog to start with "RNAseq data analysis". This blog is active on twitter too. I find this blog really helpful. **http://www.rna-seqblog.com/** Hope this helps. ...
written 2.1 years ago by Samarth Kulshrestha200
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Comment: C: Regarding Split reads and discordant reads
... Deepika, You just follow any structural variation (SV) detection method paper, that will give you a clear idea about how to look for SV signatures using Discordant reads. Choose your SV caller carefully. Best. ...
written 2.1 years ago by Samarth Kulshrestha200
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Comment: C: Regarding Split reads and discordant reads
... Deepika, Output mentioned by you seems to have multimapped property (read mapping to multiple locations of the genome: You can check multimapped property by looking at XA tag). In your first DISCORDANT read: check XA tag (pasted below) xa:z:ch="" r05,+46698740,111m4d28m12s,13;chr06,-30674967,12s2 ...
written 2.1 years ago by Samarth Kulshrestha200
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Answer: A: Regarding Split reads and discordant reads
... For Paired-end data generated by high-throughput sequencers, there are two different types of read categories: **1) Concordant reads (Properly aligned reads)** **2) Discordant reads (improperly aligned reads: important to identify genome alteration events)** **Concordant reads:** ha ...
written 2.1 years ago by Samarth Kulshrestha200
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Comment: C: problem with piping samtools sort
... To include header section to your output BAM run samtools command: - **samtools -bhS yourfile.sam > yourfile.bam** Here parameter indicates that - b: your output will be in BAM format - h: print header for the SAM output - S: input is SAM After performing this step, sort **yourfile.bam** ...
written 2.1 years ago by Samarth Kulshrestha200
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Answer: A: problem with piping samtools sort
... Yor error message hints that your generated output BAM is without header section. Please check for header section using command below **samtools view -H yourfile.bam** Above command should print Header only (No alignment section) ...
written 2.1 years ago by Samarth Kulshrestha200
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Comment: C: How to run a Perl script
... I can find out that your script is a part of a package called "ea-utils". Below is the link to the package: Step1: Just download the package from the given link below. **https://github.com/ExpressionAnalysis/ea-utils** Step2: Unzip the package Step3: Just compile and install it using the instruct ...
written 2.1 years ago by Samarth Kulshrestha200

Latest awards to Samarth Kulshrestha

Popular Question 2.0 years ago, created a question with more than 1,000 views. For PatternCNV : tool detects DNA copy number of variations
Scholar 2.1 years ago, created an answer that has been accepted. For A: Extracting coverage per base pair
Scholar 2.2 years ago, created an answer that has been accepted. For A: Extracting coverage per base pair
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Germline CNV caller
Popular Question 5.5 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 5.7 years ago, has more than 80 characters in the information field of the user's profile.

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