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Old 04-26-2014, 01:51 PM   #1
sincity1821
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Location: USA

Join Date: Apr 2014
Posts: 2
Default Introduction

I am an undergraduate student at UNLV and am taking a Bioinformatics class. We just recently had our exomes sequenced and were given the fastq file that we are required to analyze and do a final project on. I have so far aligned the file to the human_g1k_v37 genome and have the sam, bam, and vcf files.

I am now at a loss as to what to do next because I am pretty new to using Notepad C++ and linux. I have been trying tutorials online but they are still advanced to me. If anyone has any help to offer please feel free to PM me!

Thank you in advance and I look forward to speaking with you!
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Old 04-26-2014, 02:05 PM   #2
dickie_ho
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Location: Newcastle Australia

Join Date: Mar 2013
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The sky is the limit my friend ...... depends what you would like to look at ... check out SnpEff
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Old 04-26-2014, 02:13 PM   #3
sincity1821
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I would like to create a phylogenetic tree based on SNPs and compare my exome as well as my classmate's exomes with say Neanderthals.

Another idea is to identify haplogroups and compare ancestral migration.

I mainly struggle in knowing how and what to compare because the files are so large and many programs that are available to do these tasks cannot handle such large files on my computer. I have access to the supercomputer on campus but am forced to run all programs using a terminal and my coding isn't exactly great. I need something that literally walks me through the basics of doing these things, step-by-step.

I know this is asking for a lot lol
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Old 04-26-2014, 02:32 PM   #4
dickie_ho
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lol sorry dude( i assume you are a guy) ... all i can say is you have to learn it yourself.. no one/ or one tutorial is going to show you step by step ... mostly because it very complex and a crap load of work involved.. what type of class is this -- wish my undergrad degree had a cool project like this ??

If you can't using a cluster, i would give up on the idea of looking at haplotypes etc .. phylogenetic tree and comparing to different species is out of my area ( maybe PCA?) ... but if you are comparing the same species -- use the GATK package which i assume would be in your exome-seq pipeline ...... slit everything up via chromosomes if you are not using a cluster, might make life a little easier

If you are actually going to do bioinformatics after undergrad its takes a long time to learn (2 years for me so far) ... and you really need to learn a programming language (i use python) and you must learn how to use a cluster..... but once you get a basic understanding of how to use the different platforms etc its very very powerful and rewarding

Sorry i can't help you much ... Good luck on the assignment
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Old 05-07-2014, 10:39 AM   #5
create.share
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Location: Spain

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Hei sincity!
I am new here also and I am also doing some programming. The program I am building now is also for FastQ. I have been on this forum less than 10 minutes and already found people with common interest!
Cool.
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Old 05-13-2014, 08:41 AM   #6
Fourval
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Location: Colorado

Join Date: May 2014
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Default What it is

Hello everybody,

I am a post-doc trying to devolop a whole genome MLST approach (with WGS data) for highly monomorphic pathogens.

Software is limited so I have been slogging through stand alone blast and rudimentary BioPerl modules and so far it seems to be promising.

Looking forward to learning and sharing!
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alignment, exome, fasta format, sequence analysis

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