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Old 04-08-2015, 12:27 PM   #1
monikajb
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Default Illumina data analysis with fastq files

Hiii all ...how should I deal with fast files or vcf files that are generated from illumina re-sequencing...i want to analyze the data but don't know how to go about it..thank you
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Old 04-08-2015, 02:52 PM   #2
GenoMax
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If you have both fastq (original data) and VCF (variant calls) files then someone must have already analyzed your data for you. Are you looking to reproduce that analysis?

Start here: http://en.wikibooks.org/wiki/Next_Ge...cing_%28NGS%29 Ask questions when needed.
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Old 04-09-2015, 07:56 AM   #3
monikajb
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yes GenoMax..i want to reproduce the results? I am trying to use igv (broad institute) but it is giving errors
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Old 04-09-2015, 08:03 AM   #4
GenoMax
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Are you just trying to visualize the alignments/SNP's? What kind of errors are you getting with IGV?

There are several steps involved in going from the original (fastq) data to vcf files (and visualization).
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Old 04-09-2015, 08:31 AM   #5
monikajb
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Thanks for the reply. I am trying to identify differences between reference genome and mutant genomes (SNPs and alignments). The error that I get is
File: /Users/Monika/Downloads/B768_S13.bam does not contain any sequence names which match the current genome. File: *****NC-000913-3, Genome:
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Old 04-09-2015, 08:47 AM   #6
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Can you ask whoever did the analysis as to what genome build they used for the analysis? Most commonly used genomes (think model organisms) are built into (or are downloadable in) IGV. Otherwise you will need to have a sequence file available with a genome name that matches the entries in the BAM file. Be sure that you have selected that genome in IGV before you open your BAM file.
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