BOL: Related items

Porechop: tool for finding and removing adapters from Oxford Nanopore reads

Rahul Nayak — Tue, 29 May 2018 07:33:44 -0500

Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.

Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

Address of the bookmark: https://github.com/rrwick/Porechop

JAMIA HAMDARD Bioinformatics Faculty Jobs 2014

Sat, 20 Sep 2014 21:00:05 -0500

JAMIA HAMDARD

(Deemed University)

Hamdard Nagar, New Delhi – 110 062

R E C R U I T M E N T

(Advertisement No. 5/2014)

Applications on prescribed form are invited for filling up the following teaching positions in the Department of Biotechnology, Faculty of Science in the university. Eligible candidates may apply on or before 30.09.2014.

1. Professor/Associate Professor - One in Pay Band of Rs. 37400-67000+ AGP Rs.10000/9000

2. Assistant Professor - Two in Pay Band of Rs. 15600-39100+ AGP Rs. 6000/-

ASSISTANT PROFESSOR – 02 (including 01 SFS)

Specialization : Bioinformatics

Qualification and Experience :

Ph.D. in Biotechnology or an allied discipline with M.Sc. in Biotechnology/ Biochemistry in the First division or equivalent grade from a recognized University/ Institute.

NET in Life Science or allied discipline in addition to the above qualification.

Experience : At least two years of Post-doctoral teaching and/or research experience in Bioinformatics or relevant field in a UGC recognized Institution of repute or international research institute/ University. Proof of research to be evidenced by publications in SCI-indexed journals of high impact factor as the first or corresponding author.

Note : University may consider exempting candidates from NET, who has been awarded Ph.D. degree from ‘A’ Grade accredited University following the procedure as notified by the UGC in its Regulations of 2009 and adopted by Jamia Hamdard.

For more information: http://www.jamiahamdard.ac.in/PDF/Online%20application%20form%20_Teaching_1.pdf
http://www.jamiahamdard.ac.in/PDF/PBAS.pdf

RNA-seq Analysis Workshop Course Materials

Jit — Tue, 03 Jul 2018 08:14:14 -0500

RNAseq can be roughly divided into two "types": Reference genome-based - an assembled genome exists for a species for which an RNAseq experiment is performed. It allows reads to be aligned against the reference genome and significantly improves our ability to reconstruct transcripts. This category would obviously include humans and most model organisms but excludes the majority of truly biologically intereting species (e.g., Hyacinth macaw); Reference genome-free - no genome assembly for the species of interest is available. In this case one would need to assemble the reads into transcripts using de novo approaches. This type of RNAseq is as much of an art as well as science because assembly is heavily parameter-dependent and difficult to do well. In this lesson we will focus on the Reference genome-based type of RNA seq. http://chagall.med.cornell.edu/RNASEQcourse/

Address of the bookmark: http://chagall.med.cornell.edu/RNASEQcourse/

Joao Pedro de Magalhaes Lab

Fri, 26 Sep 2014 19:08:34 -0500

Ageing has a profound impact on human society and modern medicine, yet it remains a major puzzle of biology. The goal of my work is to help understand the genetic, cellular, and molecular mechanisms of ageing. In the long term, I would like my work to help ameliorate age-related diseases and preserve health. No other biomedical field has so much potential to improve human health as research on the basic mechanisms of ageing. Please see our lab website for further details about our work and publications.

Functional and Comparative Genomics

http://jp.senescence.info/
http://www.senescence.info/
http://www.liv.ac.uk/integrative-biology/staff/joao-de-magalhaes/

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

ComparativeGenomics Exercise2

Neel — Wed, 22 Aug 2018 22:10:56 -0500

COMPARATIVE MICROBIAL GENOMICS ANALYSIS WORKSHOP @ cbs.dtu.dk

Free Bioinformatics workbench https://www.mn.uio.no/ifi/english/research/networks/clsi/earlier_seminars/2012/tammivesth_osloseminarfinal.pdf

Ensembl 77 has been released!

Seema Singh — Sun, 05 Oct 2014 16:38:58 -0500

New updates in e!77 !!

Updated human gene set (GENCODE 21)
Updated rat gene set including manual annotation from HAVANA
New species: Vervet-African green monkey
Imported Transcript Support Levels (TSLs) from UCSC for human and mouse
Imported APPRIS flag for human and mouse
Updated Amazon molly gene set

Find more at http://www.ensembl.info/blog/2014/10/02/ensembl-77-has-been-released/

BASE: a practical de novo assembler for large genomes using long NGS reads

Rahul Nayak — Fri, 19 Oct 2018 07:25:21 -0500

new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs.

Address of the bookmark: https://github.com/dhlbh/BASE

CANU genome assembly parameters !

Rahul Nayak — Mon, 07 Jan 2019 08:40:37 -0600

Choose the appropriate parameters to run Canu and run it. The assembly will take about an hour. You can use two cores (parameter -maxThreads=2) and you would like to disable cluster option, since we compute on a single Amazon server set off the option to compute on cluster useGrid=false. This specifications should be for your project discussed with a local computing guru. The parameters that are in square brackets [] are optional, symbol | stands for "or".

usage:   canu [-correct | -trim | -assemble | -trim-assemble] \
              [-s ] \
               -p  \
               -d  \
               genomeSize=[g|m|k] \
               -maxThreads=2 \
               useGrid=false \
              [other-options] \
               read_file.fastq.gz

A default Canu run produces usually high quality assembly, example of a command that was used for testing can be found below. However, there are still a lot of parameters that are possible to tweak. For example if we desire to assemble haplotypes separately of if we want to smash them together, we can alternate the error correction process.

canu -p test_asmbl \
     -d asm_test3 \
     genomeSize=2m \
     -maxThreads=2 useGrid=false \
     -pacbio-raw \ ~/pacbio/dna/sample_reads.fastq.gz

There is a brilliant section in documentation about parameter tweaking.

The output directory contains will contain many files. The most interesting ones are:

*.correctedReads.fasta.gz : file containing the input sequences after correction, trim and split based on consensus evidence.
*.trimmedReads.fastq : file containing the sequences after correction and final trimming
*.layout : file containing informations about read inclusion in the final assembly
*.gfa : file containing the assembly graph by Canu
*.contigs.fasta : file containing everything that could be assembled and is part of the primary assembly

The basic stats of assembly can be read from reports generated by the assembler, or calculated using standard UNIX command line tools.

More at https://canu.readthedocs.io/en/latest/faq.html

JRF/SRF at University of Hyderabad

Fri, 17 Oct 2014 01:55:44 -0500

Applications are invited for the following post of Junior Research Fellow (temporary position coterminous with the project) under DBT funded research project on ““Understanding the functions of α1β1γ1/α2β1γ1 selective AMPK Modulators in dissecting the pharmacological role of these isozymes in metabolic diseases”

Qualified and interested candidates can send their curriculum vitae by e-mail to hr@drils.org on or before 27th October 2014 mention in the subject line of the mail the following code: AMPK-Biology.

Selected candidates will be called for a personal interview to Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad. The selected candidate is expected to report within two weeks from the date of selection to start work on the project.

Junior Research Fellowship (Molecular Modeling/Biology) for two years and Senior Research fellowship for one year

Junior Research Fellowship: Rs. 15,600/- (consolidated) per month for first two years.
Senior Research Fellowship: Rs. 18,200/-(consolidated) per month for the 3rd year.

Duration: The duration of the fellowship is for three years. However, the performance of the candidate will be reviewed after the completion of every year and the fellowship will be renewed only upon satisfactory performance.

Responsibilities:

1) Literature search.
2) Design, plan and execute experiments under the supervision of the scientist.
3) Provide scientific support to the scientist in his/her research activities.
4) Book keeping and maintenance of stocks and consumables.

Essential Qualifications:

Required: M.Sc. in Microbiology/Biotechnology/Bioinformatics or any other related branch of basic Sciences from a recognized university/institute with a consistent academic record of minimum 60% aggregate in all qualifying examinations. The candidate should be NET qualified for lectureship. The candidate should be motivated to work with dedication.

Desirable: expertise/experience in both Molecular Modeling and Molecular Biology.

Experience: 0-2 years in the areas of Molecular Modeling and/or Molecular Biology and cell biology and Biochemistry.

Preferable: Relevant research experience as evident from thesis/dissertation/project work.

Advertisement: http://www.ilsresearch.org/userfiles/Junior%20REsearch%20Fellowship%20-%20AMPK(Biology).pdf