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Old 02-03-2010, 03:34 PM   #1
Location: San Diego

Join Date: Jan 2010
Posts: 15
Default Extracting contig info and singletons


Our lab recently received 454 sequences back from Roche, and the files came in two types: all reads, and assemblies.
Should we have expected to also receive file(s) containing the singleton reads that didn't make it into the contigs? It seems to me such files would have been generated as a result of the assembly process, but we don't have them. We also don't have any info on the number of reads composing each contig.

Does anyone have any general insights or similar experiences?

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Old 02-05-2010, 03:21 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

Our local sequencing centers will generally us 454 data as the raw SFF file, plus the reads as FASTA with QUAL files (redundant if you can cope with the SFF file), plus a folder with all the output from running it through Newbler to give a draft assembly (redundant if you have the resources to run Newbler or other tools yourself). For example, the file 454ReadStatus.txt tells you which reads were used in contigs, were singletons, or were discarded.

Some sequencing centers will also generate some basic graphs, for example looking at the read lengths or contig lengths as a very simple way to gauge the overall quality/volume of output.

If you plan to do your own assembly or other analysis, I would ask for the raw SFF file.
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Old 08-20-2011, 06:44 AM   #3
Location: India

Join Date: Jun 2010
Posts: 20

Could somebody explain in detail about 'Singleton' reads and how they can be identified in the 'all reads' file. Also how useful it is to filter the singletons?
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Old 09-09-2011, 04:25 AM   #4
Junior Member
Location: Germany

Join Date: Jun 2011
Posts: 6

Hi maubp,

i have sff files from 454 and want to use CLC for de novo assembly and further analysis, I wana ask that what's the difference if I map my contigs to reference or do BLAST??????
what you could recommend the settings for de novo assembly?????????
waiting for reply
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Old 09-09-2011, 05:03 AM   #5
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

What's that got to do with this thread (Extracting contig info and singletons) AAWT?

Maybe you should start a new thread with more details about your problem.
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