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Old 01-20-2010, 12:30 PM   #1
JonB
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Location: Norway

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Default Newbler assembly - excluding specific reads?

Hi,

I have sequenced genomic DNA from a eukaryote and have ran a newbler assembly of the sff file from the 454 lab. Some of the contigs are clearly belonging together, but are not assembled into one. This seems to be caused by a few reads that looks like artefacts from the genomic amplification. (These reads are split into two and the two halves match each end of the contig, like a circle.)

I wonder if it is possible to run newbler and to specify that these reads (i have the names) should not be considered?

Thanks!

Jon
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Old 01-20-2010, 02:35 PM   #2
kmcarr
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Jon,

Yes, you can exclude specific reads from the assembly. Create a text file with the read names you wish to exclude, one name per line, nothing else. When you run newbler use the parameter '-fe <filename>' where filename is the file described above.
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