User: Praneet Chaturvedi

Reputation:
120
Status:
Trusted
Location:
Cincinnati Children's Hospital and Medical Center
Twitter:
praneet006
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
2 years, 5 months ago
Email:
p*********@gmail.com

Praneet is currently working as Senior Analyst Bioinformatics for the Division of Developmental Biology at Cincinnati Children's Hospital and Medical Center. Praneet has wide range of experience in the bioinformatics specializing in genomics. Praneet has vested experience in developing, maintaining and optimizing workflows for NGS datasets. Praneet also has experience in tool development and is developer of Computational Suite for Bioinformaticians and Biologists. Along with the above Praneet works closely with principal investigators and help them in their research and grants by developing customized bioinformatics solutions and interpreting results.
Praneet believes in learning and is ever-evolving with the learning curve.
#Bioinformatics #NGS #Genomics #MachineLearning #DataScience

Posts by Praneet Chaturvedi

<prev • 14 results • page 1 of 2 • next >
0
votes
2
answers
271
views
2
answers
Comment: C: Align RNA-seq data to a custom list of exons?
... I agree with Nicolas. Adding custom transcript annotations to the gtf is correct way forward. One thing to remember is to add the fasta sequence of custom exon annotations to their specific start positions in the chromosome/scaffold of interest in the genome .fa file. ...
written 10 months ago by Praneet Chaturvedi120
1
vote
3
answers
1.2k
views
3
answers
Answer: A: NCI-60 RNA-seq data
... You will need dbGAP access to retrieve data from SRA of this kind. This data I think was not submitted using normal SRA portal and was submitted through dbGAP portal : https://www.ncbi.nlm.nih.gov/sra/docs/submitdbgap/ Cheers !! ...
written 10 months ago by Praneet Chaturvedi120
1
vote
1
answer
615
views
1
answers
Comment: C: How to treat the pair-end files as single-end when RNA-Seq align?
... First of all, if you have paired-end data then you why you want to process them as single end. Paired end data provides you with better mappability and alignment as you have two mates to support the mapping. I provided solution in case of the pairs is not sequenced correctly or you have a mix of pa ...
written 10 months ago by Praneet Chaturvedi120
1
vote
1
answer
615
views
1
answers
Comment: A: How to treat the pair-end files as single-end when RNA-Seq align?
... Treat each pair as a single end fastq and after quantification you can take the average of the TPM/RPKM/FPKM of the read pairs. Cheers !! ...
written 10 months ago by Praneet Chaturvedi120
1
vote
2
answers
393
views
2
answers
Answer: A: IGB crashes when loading track or trying to navigate along the genome
... Please update your java to latest and uninstall IGV and reinstall latest version of IGV Cheers !! ...
written 10 months ago by Praneet Chaturvedi120
2
votes
1
answer
1.1k
views
1
answers
Answer: A: Batch effect correction in DE analysis of single cell RNA-seq data and visualiza
... Please use SVA package in R : https://bioconductor.org/packages/release/bioc/manuals/sva/man/sva.pdf SVA can help you with identifying surrogate variables in the data and also account for batch effect removal using COMBAT SVA is easy to use and if you find no surrogate variables then just use betw ...
written 10 months ago by Praneet Chaturvedi120
1
vote
3
answers
924
views
3
answers
Answer: A: macs2 conda installation problem
... sudo pip install MACS2 This should be able to install macs2. Please update following before trying: 1) pip install --upgrade pip 2) pip install numpy 3) pip install --upgrade numpy Cheers !! ...
written 10 months ago by Praneet Chaturvedi120
0
votes
1
answer
1.3k
views
1
answers
Answer: A: Find Transcription factor binding site for a gene list
... You can use [Homer's capability to get TF binding sites in the promoter regions of genes of interest][1] There are some databases as well: 1. [TF2DNA][2] [Allows batch search] 2. [CISBP][3] [requires sequences of promoters] Cheers !! [1]: http://homer.ucsd.edu/homer/microarray/index.html [2]: ...
written 10 months ago by Praneet Chaturvedi120 • updated 10 months ago by RamRS24k
0
votes
0
answers
538
views
0
answers
Tool: Computational Suite for Bioinformaticians and Biologists
... Version3.0 is now available for download !! Download CSBB-v3.0 from GitHub or Source Forge : GitHub : https://github.com/csbbcompbio/CSBB-v3.0 Source Forge: https://sourceforge.net/projects/csbb-v3-0/?source=navbar Major Highlights of version 3.0: *RNA-Seq processing for human, mouse, frog and ze ...
0
votes
5
answers
6.1k
views
5
answers
Answer: A: Peaks And Nearby Genes
... HOMER : http://homer.ucsd.edu/homer/ngs/annotation.html Inputs : peak file and genome build ...
written 2.3 years ago by Praneet Chaturvedi120

Latest awards to Praneet Chaturvedi

Popular Question 10 months ago, created a question with more than 1,000 views. For CSBB-v2.0 [Computational Suite for Bioinformaticians and Biologists version 2]
Popular Question 12 months ago, created a question with more than 1,000 views. For CSBB-v2.0 [Computational Suite for Bioinformaticians and Biologists version 2]
Autobiographer 16 months ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1772 users visited in the last hour