non paired adapters in 454 data

donniemarco · 10-16-2009, 11:26 AM

Can anyone please let me know any preprocessing steps (like cleansing adapters or any other steps) for non paired 454 sequenced data and any available tool that allows the same, before assembling is performed.
Thanks

sklages · 10-18-2009, 10:42 PM

This all depends heavily on what kind of library (ESTs, gen. shotgun, fosmid pool etc) you are using. This decides if you have any kind of vector and/or adaptors to be removed. If your library is free of any unwanted sequence and you don't see the need for screening before assembly, then fine, go for it.

If not, tools like SSAHA (Sanger Centre), cross_match (WashU), megablast (NCBI) might be of assistance. There are many more.

Some assemblers also provide some kind of clipping functionality (e.g. MIRA).

cheers,
Sven

donniemarco · 10-19-2009, 07:55 AM

Thanks for your reply. It was really helpful.

What about PolyA and PolyT sequences? How long any sub-sequence be to qualify as polyA or polyT.

sklages · 10-19-2009, 09:33 AM

Depends on your type of library and on the quality of the reads. Give it a try, play around.

Sven

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10-16-2009, 11:26 AM	#1
donniemarco Member Location: USA Join Date: Aug 2009 Posts: 17	non paired adapters in 454 data Can anyone please let me know any preprocessing steps (like cleansing adapters or any other steps) for non paired 454 sequenced data and any available tool that allows the same, before assembling is performed. Thanks

10-18-2009, 10:42 PM	#2
sklages Senior Member Location: Berlin, DE Join Date: May 2008 Posts: 628	This all depends heavily on what kind of library (ESTs, gen. shotgun, fosmid pool etc) you are using. This decides if you have any kind of vector and/or adaptors to be removed. If your library is free of any unwanted sequence and you don't see the need for screening before assembly, then fine, go for it. If not, tools like SSAHA (Sanger Centre), cross_match (WashU), megablast (NCBI) might be of assistance. There are many more. Some assemblers also provide some kind of clipping functionality (e.g. MIRA). cheers, Sven

10-19-2009, 07:55 AM	#3
donniemarco Member Location: USA Join Date: Aug 2009 Posts: 17	Thanks for your reply. It was really helpful. What about PolyA and PolyT sequences? How long any sub-sequence be to qualify as polyA or polyT.

10-19-2009, 09:33 AM	#4
sklages Senior Member Location: Berlin, DE Join Date: May 2008 Posts: 628	Depends on your type of library and on the quality of the reads. Give it a try, play around. Sven