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Old 11-22-2010, 01:19 PM   #1
zhuz
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Default data format from illumina solexa

Hi everyone,

I am new here, and also new to this field of the next generation sequencing. I have a simple question: What is the format of sequences data those we get from illumina sequencing? Is it fasta?

thanks

zhuz
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Old 11-22-2010, 02:38 PM   #2
drio
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Most people uses qseq (raw reads + basecall qualities) or sequence files (fastq format with reads that passed the filtering criteria). Most of the downstream tools come with scripts to convert from qseq to fastq as necessary. Also, fastx seems to be used a lot around here.
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Old 11-23-2010, 07:25 AM   #3
zhuz
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Thank you drio. Your information is very helpful.
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Old 11-26-2010, 10:32 AM   #4
SillyPoint
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You should also be aware of the (relatively) new SAM/BAM format. It (optionally) includes alignment information, in addition to sequence and quality. There are lots of tools for manipulating data in SAM format.

See:
http://samtools.sourceforge.net
http://samtools.sourceforge.net/SAM-1.3.pdf

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Old 12-21-2010, 12:52 PM   #5
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Qseq is what would be common between different Illumina systems, but one could configure to get fastq or Illumina native(previously called SCARF) from the qseq files. Qseq's will generally be too many in number per channel per barcode, but a fastq or Illumina native is particularly consolidated and easy to perform data analysis on.
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