Problems with the illumina .fastq sequence data annotation

tractorsazi · 01-30-2012, 05:34 AM

Does anyone know how I can annotate the .fastq file data resulted from illumina sequencing? I know thw Galaxy portal can be helpful for the trimming and grimmer for my 10 GB sequence file, but I don't know which step's result is a fasta file that is easy to use to annotation.

arvid · 01-30-2012, 06:50 AM

I'm not sure what you mean by annotation here. What do you wish to achieve with your sequence data?

tractorsazi · 01-30-2012, 07:43 AM

I wish to achieve a fasta file of my sequencing results with some large contigs that be useful to distinguish the ORFs and their functions using the annotation pipeline. The CLC genomics workbench has the options to achieve this goal, but the free trial version of this software which I downloaded hasn't the highthrouput analysis tool.

arvid · 01-30-2012, 07:50 AM

So you wish to de novo assemble your data.

If it is genomic data, search for "genome de novo assembly" and you'll find plenty of software (ABySS, Velvet, SOAPdenovo etc.). If it is RNA data, search for "transcriptome de novo assembly") and you find other software (e.g. Trinity, Oases, Trans-ABySS etc.).

You'll need a server with plenty of RAM and computing power to run most of these software, though... For the commercial alternatives (like CLCbio) you need some money and still a decent workstation (32 GB RAM).

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01-30-2012, 05:34 AM	#1
tractorsazi Junior Member Location: Iran - Tehran Join Date: Jan 2012 Posts: 2	Problems with the illumina .fastq sequence data annotation Does anyone know how I can annotate the .fastq file data resulted from illumina sequencing? I know thw Galaxy portal can be helpful for the trimming and grimmer for my 10 GB sequence file, but I don't know which step's result is a fasta file that is easy to use to annotation.

01-30-2012, 06:50 AM	#2
arvid Senior Member Location: Berlin Join Date: Jul 2011 Posts: 156	I'm not sure what you mean by annotation here. What do you wish to achieve with your sequence data?

01-30-2012, 07:43 AM	#3
tractorsazi Junior Member Location: Iran - Tehran Join Date: Jan 2012 Posts: 2	I wish to achieve a fasta file of my sequencing results with some large contigs that be useful to distinguish the ORFs and their functions using the annotation pipeline. The CLC genomics workbench has the options to achieve this goal, but the free trial version of this software which I downloaded hasn't the highthrouput analysis tool.

01-30-2012, 07:50 AM	#4
arvid Senior Member Location: Berlin Join Date: Jul 2011 Posts: 156	So you wish to de novo assemble your data. If it is genomic data, search for "genome de novo assembly" and you'll find plenty of software (ABySS, Velvet, SOAPdenovo etc.). If it is RNA data, search for "transcriptome de novo assembly") and you find other software (e.g. Trinity, Oases, Trans-ABySS etc.). You'll need a server with plenty of RAM and computing power to run most of these software, though... For the commercial alternatives (like CLCbio) you need some money and still a decent workstation (32 GB RAM).