newbie desperate and confused

[charsonic_wu]

Hi all,

I am completely new to sequencing.
I am a computer science student but I am working on a bioinformatics project on whole genome functional annotation.

My data is in csfasta format.
How do I change this to fasta format?
I am also very confused..what is the difference between the F3.csfasta file and the F5.csfasta file?

Additionally, I have been told that the data is in clc format..what does this mean?

Does anyone know of any good tools to do whole genome functional annotations?

I am extremely desperate and very very confused. Any information would be very much appreciated.

Thank you.

[nicedad]

Hope this helps

http://seqanswers.com/forums/showthread.php?t=1425

[BetterPrimate]

I'll hazard a guess that your csfasta files came from an ABI SOLiD sequencer so you need to do some further analysis, e.g. using the tools in ABI Bioscope package to find the SNVs and INDELs in your data. The output will then be in GFF format. Google can find a pdf of the Bioscope manual.
Once you've got your list of SNVs and filtered out the low quality reads, an easy way to annotate them is to feed the list into the online SeattleSeq Annotation tool.

[damiankao]

Read up on genome annotation first.

Then read about SOLiD sequencing.

You have SOLiD sequenced reads. F3 and F5 are the pairs of a mate pair library.

The clc files are for a bioinformatics software called CLC Bio. They are probably the mapping .sam files that has been converted to clc format.