data format from illumina solexa

zhuz · 11-22-2010, 01:19 PM

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

drio · 11-22-2010, 02:38 PM

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.

zhuz · 11-23-2010, 07:25 AM

Thank you drio. Your information is very helpful.

SillyPoint · 11-26-2010, 10:32 AM

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

--TS

spadejac · 12-21-2010, 12:52 PM

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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11-22-2010, 01:19 PM	#1
zhuz Junior Member Location: New york Join Date: Nov 2010 Posts: 3	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

11-22-2010, 02:38 PM	#2
drio Senior Member Location: 41°17'49"N / 2°4'42"E Join Date: Oct 2008 Posts: 323	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. __________________ -drd

11-23-2010, 07:25 AM	#3
zhuz Junior Member Location: New york Join Date: Nov 2010 Posts: 3	Thank you drio. Your information is very helpful.

11-26-2010, 10:32 AM	#4
SillyPoint Member Location: Frederick MD, USA Join Date: May 2008 Posts: 39	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 --TS

12-21-2010, 12:52 PM	#5
spadejac Junior Member Location: Newark, Delaware Join Date: Sep 2009 Posts: 4	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.