BOL: Related items

Live Webinar on RNA-Seq Data Analysis on 9 Nov 2016

Strand — Wed, 19 Oct 2016 05:25:27 -0500

Live Webinar on RNA-Seq Data Analysis

Abstract: Strand NGS supports an extensive workflow for the analysis and visualization of RNA-Seq data. The workflow includes Transcriptome / Genome alignment, Differential expression analysis with Statistical approach and Splicing events detection. Strand NGS also supports novel discovery like identification of novel genes, exons and Novel splice junctions, alongside it can also detect gene fusion events. Further downstream analysis such as GO and pathway analysis can be performed on the set of interesting genes. The product has an option to create pipelines for time consuming jobs which automates analysis and leaves more time for end data interpretation. This webinar will give an overview of the features in the RNA-Seq data analysis workflow in Strand NGS and also highlights on parameters within each feature that can be optimized depending on datasets and analysis needs.

Speaker: Mr. Sugandan Sivamani, Senior Application Scientist, Strand Life Sciences

Date: 9th Nov, Session 1 for SAPK/ APFO: 2:30 PM IST Date: 9th Nov, Session 2 for AFO/ EMEA: 9:00 AM PST

Clump Finding Problem Solved with Perl

Jit — Wed, 10 Jun 2015 00:17:17 -0500

The question at http://rosalind.info/problems/1d/

Script are moved to http://bioinformaticsonline.com/snippets/view/34633/clump-finding-problem-solved-with-perl

Quick next generation sequencing (NGS) terms definition

Neel — Fri, 09 Jun 2017 04:52:26 -0500

fragment size: the Illumina WGS protocol generates paired-end reads from both ends of longer fragments. The lengths of these fragments are assumed to be sampled from a normal distribution. Therefore, in the absence of structural variants, mapping locations of the paired ends span within an interval [δmin,δmax]. Most (>90%) of paired-end reads are sampled from no-SV regions, therefore the fragment size distribution can be learned empirically for each WGS data set separately.

concordant reads: a read pair is called concordant if they can be mapped to the reference genome as “expected”: (a) mapped to opposing strands where the upstream read is mapped to the forward strand and the downstream read is mapped to the reverse strand2, (b) the distance between ends is between the minimum and maximum expected fragment size.

discordant reads: briefly, any non-concordant read pair is considered discordant. Note that, by definition, the discordant read pairs signal potential SVs. The sequence signature produced by these type of reads is known as read-pair signature.

split reads: a read that can only be mapped to the reference genome by breaking into two sub-reads is called a split-read. These types of reads also indicate a potential SV or a short insertion or deletion (indel).

read depth: number of reads that map within a region of the genome. Overall genome-wide read depth is also referred to as depth of coverage. It is expected that the number of reads that “cover” each base-pair to follow a Poisson distribution. Therefore, if the read depth over a certain region deviates significantly from this distribution, it signals for a potential copy number variation (CNV).

MIX: Combining multiple assemblies from NGS data

Rahul Nayak — Tue, 08 May 2018 04:58:05 -0500

Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length.

The Mix algorithm, approach and results were published in BMC bioinformatics : http://www.biomedcentral.com/1471-2105/14/S15/S16.

Address of the bookmark: https://github.com/cbib/MIX

RA at University of Delhi

Wed, 17 Jun 2015 20:35:35 -0500

Research Scientist Jobs opportunity in University of Delhi on temporary basis

Qualifications : Ph. D.

Desirable : Experience on DNA Markers, plant genome mapping and bioinformatics

No. of Post : 03

Department : Genetics

Salary : Rs. 60,000/-
How to apply

The applicants are requested to register their names on the day of interview in the First Floor, Biotech Centre, Centre for Genetic Manipulation of Crop Plants, Department of Genetics before the stipulated time for the interview. Only the registered eligible candidates will be interviewed on the day in the Committee Room. Applicants are requested to bring all related documents, in original and a set of photocopy, for verification. Date and time of the interview : 25.06.2015 at 10:30 AM.

Click Here for Job Details http://www.du.ac.in/du/index.php?mact=News,cntnt01,detail,0&cntnt01articleid=5492&cntnt01returnid=83

HALC: High throughput algorithm for long read error correction

Jit — Fri, 08 Jun 2018 10:47:41 -0500

HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long read region can be aligned to at least one contig region, including its true genome region’s repeats in the contigs sufficiently similar to it (similar repeat based alignment approach) HALC was able to obtain 6.7-41.1% higher throughput than the existing algorithms while maintaining comparable accuracy. The HALC corrected long reads can thus result in 11.4-60.7% longer assembled contigs than the existing algorithms.

Address of the bookmark: https://github.com/lanl001/halc

At what age did you gain passion in Bioinformatics?

Jit — Tue, 23 Jun 2015 10:39:06 -0500

Most of the bioinformatician were biologist ( yeah ... not all ;), and at later stage they gain a passion in Bioinformatics and learn it. When did you get inclined towards computational analysis of biological data?

Convert EnsEMBL GTF to Annotation table (Geneid, GeneSymbol, GeneWiseChrLocation, GeneClass, Strand) Raw

EagleEye — Fri, 24 Jun 2016 18:08:49 -0500

Bash Script source:

https://gist.github.com/santhilalsubhash/367befcf5216be4b1fd9

Information:

This script converts EnsEMBL GTF (Ex: https://gist.githubusercontent.com/santhilalsubhash/1e7cca357e52a181dc25/raw/cfb803e07900a2baefbb6534f1299fd30cb57a29/sample.GTF) file to annotation table format. It generated two files
1) Transcript wise chromosome location with information about transcripts (Ex: https://gist.githubusercontent.com/santhilalsubhash/c7dec516e0338503a4b6/raw/de0af1a39f0005c4ce7321c5ae57fc8b4a14c7f4/sample.GTF_enst_annotation.txt)
2) Gene wise chromosome location with information about genes (Ex: https://gist.githubusercontent.com/santhilalsubhash/c92006c5080f0333bec2/raw/d16e0b2440d73b09b486d3c9751cdb248a73fa0b/sample.GTF_ensg_annotation.txt)

Note: You can download GTF files from http://www.ensembl.org/info/data/ftp/index.html

RA Bioinformatics at Bharathidasan University

Sun, 28 Jun 2015 12:21:48 -0500

National Facility for Marine Cyanobacteria
Department of Marine Biotechnology
Bharathidasan University
Tiruchirappalli -620024, Tamil Nadu

Applications are invited from individuals who have high motivation to do research for the below mentioned position,

1. Research Associate - 1 No.
in the DBT sponsored project under the supervision of Dr. D. Prabaharan, Principal Investigator, National Facility for Marine Cyanobacteria, Dept. of Marine Biotechnology, Bharathidasan University, Tiruchirappalli-24.

Title of the Project: “Establishment of National Repository for Micro algae & Cyanobacteria” funded by Department of Biotechnology, Govt. of India

Qualification

1. Research Associate – 1 No. Rs. 36,000/38,000/40,000 per month for I, II and III year + 20% HRA

Essential : Doctoral degree in relevant subject from recognized University/ Institutes
Desirable: Research experience in molecular biology and bioinformatics

Interested candidates can send their complete CV in plain paper with a passport size photograph, with details of Marks secured in all subjects from plus two stage (with proof, full postal address, sex, date of birth, community etc., along with additional qualification or experiences and two address of references whom could be contacted (One of whom should be PG teacher/guide). Application should reach the Principal Investigator on or before 30.06.2015 by Email (nfmcbic@yahoo.com)/Registered post/ Speed post, with subject subscribed as “Application for Research Associate /Technical Assistant /Lab attendant”. Qualifying candidates will be short listed and communicated with date of interview. No TA and DA will be given for attending the interview. Addressfor Communication Dr. D. Prabaharan Principal Investigator National Facility for Marine Cyanobacteria Bharathidasan University Tiruchirappalli-620024, Tamil Nadu.

Advertisement: http://www.bdu.ac.in/adv/NFMC_Project_Positions.pdf

nQuire: a statistical framework for ploidy estimation using next generation sequencing

Jit — Thu, 04 Oct 2018 05:23:59 -0500

nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available at https://github.com/clwgg/nQuireunder the MIT license.

Address of the bookmark: https://github.com/clwgg/nQuireunder