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(Solved) : Bioinformatics Need Use Galaxy Set Experiment Given Files Unsure Begin Distributing Galaxy Q35533032 . . .

BIOINFORMATICS

I need to use Galaxy to set up an experiment on some givenfiles, but I am unsure how to begin.

1. I am distributing a Galaxy History called:CG19FinalProjectDNADatasets containing:
   • Sacce1_AssemblyScaffolds.fasta <- Saccharomycescerevisiae Wild-Type Genome
   • Sacce1.ExternalModels.gff3 <- Saccharomycescerevisiae Wild-Type Genome Annotations
   • Scerevisiae_RAMutant_Genome.v02.fa <- Saccharomycescerevisiae Mutant Genome
   • Sacce1_chrVI-VII-VIII.fasta <- Saccharomycescerevisiae Chromosomes VI/VII/VIII Wild-Type Genome
   • All Datasets are from the Wild-TypeGenome
   • Dataset01:
     • SRR352492.sra_1.fastq
     • SRR352492.sra_2.fastq
   • Dataset02:
     • SRR352384.sra_1.fastq
     • SRR352384.sra_2.fastq
   • Dataset03:
     • SRR452441.csra_1.fastq
     • SRR452441.csra_2.fastq
   • The Datasets have already been Quality Controlled
   • Saccharomyces cerevisiae Wild-Type ChromosomesVI/VII/VIII is being provided for you to test/optimize your mappingconditions
2. Your task is:
   • To use these NGS Datasets to identify any polymorphisms thatmight be present in theSaccharomyces cerevisiae MutantGenome
   • You are welcome to validate your findings using other methods(e.g., alignments, Blast, etc), but your primary conclusionsmust be based on NGS Reads mapping
   • Your findings must also be validated by IGVfigures displaying the presence/absence of the polymorphisms youhave identified. In other words, each polymorphism claim must besupported by an IGV figure
   • All your findings must be properlydocumented
   • A Final Project Report and FinalProject Presentation must be prepared according to theinstructions outlined below
3. Recommendations:
   • Start by looking at your data, study the data
   • Design a logical and simple Experimental Strategy. Rememberthere is no a single way to address this problem
   • Learn how to use and try to understand the following tools inGalaxy:
     • Bowtie map reads against reference genome (output = unsortedsam file)
     • Bowtie2 – map reads against reference genome (output = sortedbam file)
     • After you settle on Bowtie and/or Bowtie2, do not change thisparameter
     • Pay special attention to the options provided to generate filescontaining aligned and/or unaligned reads. Remember, you might needto use those parameters to demonstrate your assumptions or testyour hypothesis
     • sort a BAM file <= Sorting is imperative after theBam file is generated and before other processing canoccur
     • Flagstat tabulate descriptive stats for BAM dataset
     • BAM mapping statistics samtools idxstats
     • Filter BAM datasets on a variety of attributes
     • BAM-to-SAM convert BAM to SAM and SAM-to-BAM convert SAM to BAM(when needed)
   • I suggest using the test chromosome you must decide on whichone of these tools is best for you task
   • Display the data on IGV
     • When using BAM files, remember to download, in addition to theBAM file, its accompanying BAM_INDEX file
   • If you need to assemble reads, let me know, and I will show youhow to do it
   • Include Controls

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Answer to Bioinformatics Need Use Galaxy Set Experiment Given Files Unsure Begin Distributing Galaxy Q35533032 . . .