Task 2 - Data analysis Section A (genomics) Task 2 is worth 70% of the module grade; Section A is worth 60% of Task 2 and hence 42% of the total module grade. For your coursework, you will analyse next generation sequencing data and spectrometry data produced by different techniques. The coursework has two sections: Section A tests your learning in genomics (learning outcome 1). This is worth 60% of the grade for this piece of coursework. Section B tests your learning in proteomics (learning outcome 3). This is worth 40% of the grade for this piece of coursework. You will be given an individual dataset for each section. This document contains the brief for Section A. Dr David Smith will provide the brief for Section B. You must perform the analyses yourself and write methods, results and answers in your own words. Doing the analysis yourself and writing in your own words is important because we are assessing whether you are able to perform the analysis and if you have understood the ideas you have been learning about. You may not pass if you simply copy sections of writing/speech from slides, lectures or videos. Grading Grading is based on the Universitys Masters level grade descriptor. This descriptor is included at the end of this document to help you understand what is expected for each grade. Section A - Genomics Your data are from Illumina paired-end sequencing of one human. You should analyse these resequencing data to

• get a list of genomic variants
• summarise the variants

Part 1: Producing a list of the individuals genomic variants Instructions Start by creating a directory for this coursework inside your home directory. All the files you produce should go into this folder. You should not copy the raw data files into this folder, use the raw data files as input by providing their file path. Make a text file (in MS Wordpad, Apple TextEdit, notepad++ or another software). On the first line of the text file state which directory you are working in. Copy each command into the text file as you run them. Check that the command is written exactly as you gave it on the command line. Make sure there are no typos and no spelling has been autocorrected. This is very similar analysis that you did with a practise dataset in the computer practicals. You should do the computational steps that are needed to produce a list of variants (some exericses we did in the practicals were to help you understand the format and contents of file types, you do not need to repeat those exercises). Submit

• Your text file of commands.

You do not need to include commands such as ls or pwd that you used to check files were produced or where you were. The commands should be those that are necessary for someone to generate a file with the same variants as you produced. Part 2: Summary of the variants detected Instructions Investigate the types of variants that were found and report how many were of each type (e.g. the number that were SNVs and the number that were indels). There are many ways of classifying variants and you should decide yourself how to do this (by thinking about what aspects of variants is most interesting). ANNOVAR can annotate variants with a lot of information. In human genomics, we are usually interested in the variants that are most likely to cause disease. You should present your results in a table and you can classifiy variants a few ways but the table should take up no more than half a page. The counting can be done in Excel, which will be demonstrated in class. Credit will be given for working out a bioinformatics method to do this (such as using software or writing a script). Submit

• A description of how you obtained the number of variants of each type.

Make sure that you describe everything that you did to get the numbers. The reader should be able to follow the description to get the same numbers as you obtained. (If you ran software on the command line or wrote a script, include the commands/script as an additional text file). Maximum half a page.

• A table of your results. Maximum half a page.

Grading for section A To grade you, the module tutors will look at the files you have produced on the Linux server and the accuracy of the commands you have submitted (both that the command would run as required and that they would generate the files that are in your coursework directory). We will assess the categories of variants you have chosen, how you have performed the classification and how clearly and completely you have described your method. Assessment of work for the module will be moderated by the internal moderator and the external examiner, as for all other assessed work on your course. Details about the format of submission for section A and how to submit You should submit

• One Microsoft Word document
• A text file for Section A Part 1

Name this file as your student number followed by _g_and_p_commands.txt

• (You can submit a text file for Section A Part 2 if you used a bioinformatics method; name the file as your student number followed by _g_and_p_commands_2.txt).

Instructions for the Microsoft Word document

• Name it as your student number followed by _g_and_p_task_2_sect_A.docx
• Put the Task 2 feedback form at the start of the document
• Use font size 12, with 1.5 line spacing for text Use single line spacing for tables
• Make sure you keep to all the page limits.
• Write in scientific language.
• Use the APA 6 format for any citing and references.

The feedback form is on the module blackboard inside the Assessment section and then the folder Task 2 - data analysis. Fill in your information on the feedback form including your course, the identifier (ID) for your sequence for Section A and the identifier for your dataset for Section B. Upload BOTH your Microsoft Word document and your text file at the online submission. (If you have a second text file, this should also be uploaded to the submission point). The submission point is inside the Assessment section of the blackboard site; click on 002 Critical Analysis - Submission Point. We recommend that you do not leave submitting your work until just before the deadline. After making a submission you are still able to upload another version until the deadline. We will mark the last attempt for each document uploaded by the deadline. You will need to submit a separate document at the same time containing your answer to Section B Dr David Smith will give you details of this. You should also upload your final submitted version of the Microsoft Word document to Turnitin. This must exactly match the lastest version submitted by the deadline. Do not submit your text file to Turnitin (if you have a second text file do not submit this to Turnitin either). Turnitin is also accessed through the Assessment section. Click on Turnitin Submissions, find the section named Task 2 section A genomics data analysis Turnitin submission and click on >>View/Complete in that section. The Turnitin submission does not have to be by the deadline but should be done as soon as possible afterwards. Turnitin checks your work for plagiarism. Plagiarism is cheating and we take it very seriously. If you are suspected of plagiarism you can be asked to attend an Academic Conduct Panel and your grade may be reduced. Level 7: Generic grade descriptor: relationship of grades of achievement to percentage mark ranges and categorical grades (CG)

Class	Category	Grade	%	General Characteristics
Distinction (Exceptional)	Exceptional Distinction	16	82	Exceptional breadth and depth of knowledge and understanding evidenced by own independent insight and critical awareness of relevant literature and concepts at the forefront of the discipline; evidence of extensive and appropriate independent inquiry operating with advanced concepts, methods and techniques to solve problems in unfamiliar contexts; Cogent arguments and explanations are consistently provided using a range of media demonstrating an ability to communicate effectively in a variety of formats using a sophisticated level of the English language in an eloquent and professional manner to both technical and non-technical audiences; a sustained academic approach to all aspects of the tasks is evidenced; academic work extends boundaries of the disciplines and is beyond expectation of the level and may achieve publishable or commercial standard.
Distinction (Excellent)	High Distinction	15	78	Excellent knowledge and understanding evidenced by some clear independent insight and critical awareness of relevant concepts some of which are at the forefront of the discipline; evidence of appropriate independent inquiry operating with core concepts, methods and techniques to solve complex problems in mostly familiar contexts; Arguments and explanations are provided that is well-supported by the literature and in some cases uses a range of media demonstrating an ability to communicate effectively in a limited number of formats using own style that is suited to both technical and non-technical audiences; a sustained academic approach to most aspects of the tasks is evidenced; one or more aspects of the academic work is beyond the prescribed range and evidences a competent understanding of all of the relevant taught content.
Mid Distinction	14	75
Low Distinction	13	72
Merit (Good)	High Merit	12	68	Very good knowledge and understanding is evidenced as the student is typically able to independently relate taught facts/concepts together some of which are at the forefront of the discipline; evidence of some competent independent inquiry operating with core concepts, methods and techniques to solve familiar problems; Arguments and explanations are provided that are typically supported by the literature and in some cases may challenge some received wisdoms; competently uses all taught media and communication methods to communicate effectively in a familiar settings; an academically rigorous approach applied to some aspects of the tasks is evidenced; some beyond the prescribed range, may rely on set sources to advance work/direct arguments; demonstrates autonomy in approach to learning.
Mid Merit	11	65
Low Merit	10	62
Pass (Sufficient)	High Pass	9	58	Satisfactory knowledge and understanding of the area of study balanced towards the descriptive rather than critical or analytical and mostly confined to concepts that are not at the forefront of the discipline; evidence of some independent reading and research to advance work and inform arguments and approaches; Arguments and explanations are limited in range and depth although some are adequately supported by the literature albeit descriptively rather than critically; competently uses at least one taught media and communication method to communicate appropriately in familiar settings; although the approach applied to some aspects of the tasks may lack academic rigour, there are some clear areas of competence within the prescribed range. Relies on set sources to advance work/direct arguments and communicated in a way which shows clarity but structure may not always be coherent.
Mid Pass	8	55
Low Pass	7	52
FAIL (Insufficient)	Borderline Fail	6	48	Knowledge and understanding is insufficient as the student only evidences an understanding of small subset of the taught concepts and techniques; fails to make sufficient links between known concepts and facts to adequately solve relevant aspects of the brief/problem; little ability to independently select and evaluate reading/research with almost total reliance on set sources and unsubstantiated arguments/methods; communication/presentation may be competent in places but fails to demonstrate structure, clarity and/or focus; inability to adequately define problems and make reasoned judgements; the general approach to tasks lacks rigor and competence.
Mid Fail	4	45
Low Fail	2	42
FAIL (Incompetent)	Very Low Fail	1	38	Knowledge and understanding is highly insufficient as the student is unable to evidence any meaningful understanding of taught concepts or methods; very limited evidence of reading and research to advance work; inadequate technical and practical skills as the student is unable to use and apply such skills to address problems or make judgements; limited or lack of understanding of the boundaries of the discipline and does not question received wisdom; approach to learning lacks autonomy and approach to tasks is not sustained; inability to communicate coherently.
ZERO	Zero	0	0	Work not submitted, work of no merit, penalty in some misconduct cases.

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