Submitting Sequenced BACs Robert Buels SGN. Purpose and Scope Provide well-organized archive of sequencing data for the tomato genome sequencing project,

Slides:

Advertisements

Similar presentations

Web Hosting. The purpose of this Startup Guide is to familiarize you with Own Web Now's Web Hosting. Own Web Now offers two web hosting platforms, one.

Advertisements

Submitting a Genome to RAST. Uploading Your Job 1.Login to your RAST account. You will need to register if this is your first time using SEED technologies.

File Transfer Protocol. FTP (File Transfer Protocol) is used to transfer programs or other information from one computer to another. This simple tool.

Where to start?. Step 1: Register or Login 1 st time, click & register, otherwise click login and we will help you if you forget your password.

The website is !st time to log into this program, click YES.

Electronic Thesis and Dissertation (ETD) Graduate School of Biomedical Sciences.

FTP Using FileZilla CS10001 – Computer Literacy. Step 1: Understanding the Interface Quickconnect Bar Message Log Area Local site navigation (either lab.

Using FileZilla to FTP CS10001 – Computer Literacy Kent State University.

Submitting Book Chapters via Manuscript Central A Short Guide for Wiley-VCH Authors.

Online Surveys A Look at Cardiff-TeleForm Denise H. Wells Planning and Research Central Piedmont Community College.

Applying for Jobs Online An Overview. Before You Apply address address Resume Resume Work history Work history Education Education Skills.

DMT File Management Common Problems Managing DMT files –Reliable Upload –Reliable Download –Where are the files kept? –Tedious Procedures Using DOS commands.

To create an account or sign in, use either of these links.

TURNITIN Step by step……… Instructors.

Copyright© 2003 Avaya Inc. All rights reserved Upgrade to Communication Manager 2.0 with Migration to Linux 8.0 Purpose: This presentation was prepared.

1 INE 1020 Introduction to Internet Engineering Tutorial 3 Discussion on Homework 1.

ISG: Course Account Training Resources: >Tutor/TA Handbook >Training>scripts >ISG WiKi.

Accessing & Submitting Homework myitlab Microsoft Office Professional 1 CSP 1203.

Albany ePAY online for Introducing the facility to make Bacs payments directly from within your accounting application the easy and efficient way!

Setting Up DreamWeaver NOTE: Use your mouse OR page down key to advance each page.

1 Project Information and Acceptance Testing Integrating Your Code Final Code Submission Acceptance Testing Other Advice and Reminders.

XP New Perspectives on The Internet, Sixth Edition— Comprehensive Tutorial 5 1 Downloading and Storing Data Using FTP and Other Services to Transfer and.

(1) Access the Oryzabase (1) Access the Oryzabase (2) Click the.

Simplify TeleHealth - Copyright 2012 Emerge.MD inc - Confidential Single Sign On via Active Directory Federation Services 4.6 Release (March 2014) Updates.

NEW FOR 2009 Faster, Easier, Friendlier. Before you start Any student, staff, or faculty member can file an accident/incident report. Accident reporting.

 Name: Santiago Bock   Telephone:  Office Number: 5106 Sennott Square  Office Hours: Tuesdays.

Prosentient Systems DSpace © Prosentient Systems 2012 DSpace training Item submission.

INIS Input Submission INIS Training Seminar 7-11 October 2013 Vienna, Austria Serene Wong INIS Unit International Atomic Energy Agency

Electronic submission of Applications using PRIAMOS How To Guide PRIAMOS PRogramme Information and Activity Management Operational System.

BAC Sequencing and Annotation: Procedure Updates and New Tools Robert Buels.

Chapter 27 - Faxes & File Transfer (FTP) Introduction Sending a Fax –The Internet can be used to send a fax. Two fax machines can be modified to communicate.

Turnitin.com REGISTRATION. Step One—Registration  Go to—

File Transfer Protocol (FTP) FTP host stores files Client logs into host Client program sends command to get a file FTP host downloads the file with error.

FILE TRANSFER PROTOCOL (FTP) for PLATINUM ASSET DISCOVERY.

FTP Using FileZilla CS10001 – Computer Literacy. Step 1: Understanding the Interface Quickconnect Bar Message Log Area Local site navigation (either lab.

How to use WS_FTP A Step by Step Guide to File Transfer.

1 Compliance Tracking Tool Activity Entry and Progress Monitoring.

How to submit an assignment to Turn It In Log in to Turn It In and select the class Find the assignment to be submitted Click “Submit”

HOW TO FILE A WARRANTY CLAIM. Main Site Go to and click “Dealer Login” at the top right of the screen.

Thesis Defense and Submission 1 Spring  Register for Spring semester  Deadline to submit thesis to GPS: Friday, April 22 nd at NOON  Deadline.

File Transfer Protocol (FTP) CIS 130. File Transfer Protocol (FTP) Copy files from one internet host (server) to your account on another host –Need domain.

Submitting Your Thesis/Dissertation into Digital Southern.

Dept user Logs in from Home Page for tender creation Login with user name and password.

Global Rangelands Data Entry Guidelines March 23, 2015.

Best 20 jobs jobs sites.

Michigan Digital Content Access for Oakland County Educators NOTE: All of this information is available at the Oakland Schools Moodle. From the main page,

SR Course Website. The SR website can be accessed by going to wb2016.org using any number of browsers on the market including those available.

IRPS 2017 Manuscript & Platform Presentation Submission Process

Setting up FTP for CAST Click on Manage Sites

36 x 2 = ? A) 36 B) 72 C) 48 D) 76.

Projectdox User Guide.

STEPS Assessment System

Required Data Files Review

BAC Sequencing and Annotation: Procedure Updates and New Tools

CS515: Bioinformatic Algorithms

Software basics on the Internet

IRPS 2018 Manuscript & Platform Presentation Submission Process

Getting High on Search Engines with WebPositionGold

How To UPLOAD Policies.

Firstly, you need to find your journal…

NIMAC for Publishers & Vendors: Batch Delivery Procedures

Guide to Getting Started with

Yating Liu July 2018 G-OnRamp workshop

Paper Submission Process

Homework Assignment #2 SIC/XE Assembler

TURNITIN.COM Instructions

Podcast Upload Instructions website:

Submitting Assignments

Presentation transcript:

Submitting Sequenced BACs Robert Buels SGN

Purpose and Scope Provide well-organized archive of sequencing data for the tomato genome sequencing project, including:  finished BAC sequences  chromatograms  assembly files  annotations

BAC Submission Guidelines A comprehensive BAC submission format exists (see handout, pp. 4-5). If we all follow this format, the data will be much easier to work with.

Problems Not all submissions follow the submission guidelines. Irregularities in naming, directory structure, submission file contents. FTP site does not separate finished and unfinished sequences. Result: data is harder to work with than it should be!

Problems To address these problems: We improved the directory structure of the FTP site. Corrected existing submissions to follow submission guidelines. We made a new submission system that checks submission guidelines.

New FTP Structure tomato_genome/bacs/ chr01/ chr02/... chr12/ bacs.seq finished_bacs.seq README validate_submission.pl

New FTP Structure tomato_genome/bacs/ chr01/ chr02/... chr12/ bacs.seq finished_bacs.seq README validate_submission.pl all seqs

New FTP Structure tomato_genome/bacs/ chr01/ chr02/... chr12/ bacs.seq finished_bacs.seq README validate_submission.pl all seqsfinished seqs

New FTP Structure tomato_genome/bacs/ chr01/ chr02/... chr12/ bacs.seq finished_bacs.seq README validate_submission.pl all seqsfinished seqsvalidation script

New FTP Structure tomato_genome/bacs/ chr01/ unfinished/ finished/ C01HBa0088L02.all.xml C01HBa0088L02.seq C01HBa0088L02.tar.gz C01HBa0216G16.all.xml C01HBa0216G16.seq C01HBa0216G16.tar.gz...

New FTP Structure tomato_genome/bacs/ chr01/ unfinished/ finished/ C01HBa0088L02.all.xml C01HBa0088L02.seq C01HBa0088L02.tar.gz C01HBa0216G16.all.xml C01HBa0216G16.seq C01HBa0216G16.tar.gz... separate finished and unfinished

New FTP Structure tomato_genome/bacs/ chr01/ unfinished/ finished/ C01HBa0088L02.all.xml C01HBa0088L02.seq C01HBa0088L02.tar.gz C01HBa0216G16.all.xml C01HBa0216G16.seq C01HBa0216G16.tar.gz... separate finished and unfinished submission

New FTP Structure tomato_genome/bacs/ chr01/ unfinished/ finished/ C01HBa0088L02.all.xml C01HBa0088L02.seq C01HBa0088L02.tar.gz C01HBa0216G16.all.xml C01HBa0216G16.seq C01HBa0216G16.tar.gz... separate finished and unfinished submissionsequence

New FTP Structure tomato_genome/bacs/ chr01/ unfinished/ finished/ C01HBa0088L02.all.xml C01HBa0088L02.seq C01HBa0088L02.tar.gz C01HBa0216G16.all.xml C01HBa0216G16.seq C01HBa0216G16.tar.gz... separate finished and unfinished annotationssubmissionsequence

New Submission System Developed to automatically check submission formatting, analyze submissions, and publish them on the FTP site. Also improves turn-around time since it is mostly automatic.

New Submission System checks submission guidelines C01HBa0001A01.tar.gz C01HBa0001A01/ chromat_dir/ edit_dir/ phd_dir/ seq_dir/ C01HBa0001A01.seq >C01HBa0001A01 ATGCCTACGAT...

New Submission System checks submission guidelines C01HBa0001A01.tar.gz C01HBa0001A01/ chromat_dir/ edit_dir/ phd_dir/ seq_dir/ C01HBa0001A01.seq >C01HBa0001A01 ATGCCTACGAT... submission is tar.gz file, named for BAC

New Submission System checks submission guidelines C01HBa0001A01.tar.gz C01HBa0001A01/ chromat_dir/ edit_dir/ phd_dir/ seq_dir/ C01HBa0001A01.seq >C01HBa0001A01 ATGCCTACGAT... submission is tar.gz file, named for BAC self-named subdirectory

New Submission System checks submission guidelines C01HBa0001A01.tar.gz C01HBa0001A01/ chromat_dir/ edit_dir/ phd_dir/ seq_dir/ C01HBa0001A01.seq >C01HBa0001A01 ATGCCTACGAT... submission is tar.gz file, named for BAC self-named subdirectory self-named sequence file

New Submission System checks submission guidelines C01HBa0001A01.tar.gz C01HBa0001A01/ chromat_dir/ edit_dir/ phd_dir/ seq_dir/ C01HBa0001A01.seq >C01HBa0001A01 ATGCCTACGAT... submission is tar.gz file, named for BAC self-named subdirectory self-named sequence file self-named sequence

validate_submission.pl Checks the formatting of your submission. Avoids having to retry uploads to correct formatting. ~$./validate_submission.pl C01HBa0001A01.tar.gz C01HBa0088L02.tar.gz passed. ~$ On your machine...

Submission Process 1.Use validate_submission.pl to verify that your submission is properly formatted. 2.Upload with scp to upload.sgn.cornell.edu, using your login and password. 3.When finished, the submission cron job will notice it and process it.

Submission Process 4.If properly formatted, you will see it on the FTP site within hours. 5.Otherwise, you will receive an asking you to correct the format and retry the submission.

Questions? Suggestions for improvement of FTP site? Suggestions for submission process?