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Old 01-29-2010, 07:33 AM   #1
Khanjan
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Location: Atlanta

Join Date: Jan 2010
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Default Removing primers

Hey all,

I am new to using gsAssembler. I want to do an assembly of cDNA sequences. However, they have primers attached to it. I saw an option called 'Trimming database for De-Novo assembly, and provided the list of primers as an input. However, when I check the output assembly, several contigs still have those primers. How do I make sure that these are removed before assembly( I have a .sff file).
Also, I want all the contigs after assembly. The AllContig.fna in gsAssembly is not listing all the contigs ( like the singletons). How do I obtain all the contigs from the assembly?

Thanks in advance for the help,

Regards,
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Old 02-05-2010, 12:09 PM   #2
flxlex
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Default

The -v option is probably what you describe, and if it does not remove all primers I guess there is a bug in gsAssembler :-(

Singletons are not contigs (by definition, I guess), but I do understand you want to get them included in your final dataset.

Using the sffinfo trick described in the software manual on page 134 (getting the read IDs from the 454ReadStatus.txt file, make a new sff file with only the singletons, and then extracting the reads as a fasta file) would do it.
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