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Old 08-27-2012, 01:12 PM   #1
empyrean
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Default Converting 454 reads to illumina reads

Hello

i have a pipeline which works with illumina reads. When i convert the 454 reads in to fastq format and give it as input, the pipeline is not working. The average length of the sequence is 350 bp. I am planning to make them in to 100bp reads. Are there any tools out there which can do this?
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Old 08-27-2012, 04:02 PM   #2
DFJ111
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I'm not sure it's a good idea, what are you doing in your pipeline? If your pipeline assumes that all sequences are the same length (as Illumina reads are) it might have issues with the variable read lengths of 454.454 reads also have a lot of associated info (e.g. adaptors, multiplexing tags, suggested end-clips) which are useful to keep. Also not sure why you'd want to throw out an average of 250bp of sequence per read.

I can think of a lot of other details that might cause the pipeline to break, it really depends what you are doing with the reads. Can you provide more details?
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Old 08-28-2012, 12:17 AM   #3
maasha
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I am also not convinced it is a good idea to sacrifice all that information, but if you must you can use Biopieces (www.biopieces.org):

Code:
read_sff -i data.sff | extract_seq -l 100 | write_fastq -o data.fq -x
or

Code:
read_454 -i data.fna -q data.qual | extract_seq -l 100 | write_fastq -o data.fq -x
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Old 08-28-2012, 08:49 AM   #4
DZhang
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Hi empyrean,

Can you share what you plan to achieve? There may be a way to use 454 reads as is to achieve what you want. Or at least help us understand why you want to stick to your Illumina pipeline.

Best regards,
Douglas
www.contigexpress.com
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