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Old 02-24-2014, 07:13 AM   #1
thh32
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Default IDBA-UD paired end data on multiple files

I want to assemble with IDBA-UD and have no experience with it. Although my data is paired half of each pair is on one file and the other half in another with a total of 12 files (~22Gb in total). Looking around online it didn't seem as if anyone had this issue before. I was also wondering if there is a way to set the K-mer as 35 instead of having to set the mink and maxk? Any help would be greatly appreciated.

Tom
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Old 02-24-2014, 10:44 AM   #2
mastal
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For paired end reads, the R1 and R2 from each pair are usually in separate files.
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Old 02-25-2014, 12:52 AM   #3
thh32
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Ok thanks, first time using this data so was unsure. Any idea how to upload them to IDBA-UD for assembly?
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Old 02-27-2014, 01:27 AM   #4
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Anyone know? All help is appreciated.
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Old 02-27-2014, 03:09 AM   #5
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I have not used IDBA-UD.

If you have IDBA-UD installed on your computer, there is a README file in the IDBA directory, that tells you how to pre-process your data for input to IDBA. I think you need to convert fastq files to fasta, and have paired reads together in the same file. They give examples of how to do this using scripts included with IDBA.

The website gives examples of parameters used with their test datasets.

http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/
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