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Old 09-17-2012, 07:18 PM   #1
Hiroki
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Location: Japan

Join Date: May 2010
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Unhappy Combine pairend reads into one file for SOPRA

Hi there,

Sorry for a pitifully newbie question.

How can I combine two fasta files, read 1 and read2 from a Illumina pairend run into a single file as this:

>seq1read1
cagtgtcgaggaac...
>seq1read2
gatatagagatctac...
>seq2read1
cagtgtcgaggttt...
>seq2read2
gatatagagatcgta...

I want to try SOPRA and it requires the format above as matepair read input.

Thank you very much.

Hiroki
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Old 09-17-2012, 08:42 PM   #2
themerlin
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Try either shuffleSequences_fastq.pl included with Velvet or this:

http://www.ngcrawford.com/2012/03/28...red-end-reads/
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Old 09-17-2012, 11:40 PM   #3
Hiroki
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Hi themerlin,

Thanx a lot.
I will try it.

Best,

Hiroki
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Old 09-18-2012, 12:37 AM   #4
maubp
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If you want more options, try searching for interleaving, the resulting file is often called an interleaved FASTA (likewise with FASTQ), because you interleave the forward and reverse read files to combine them.
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Old 09-26-2012, 07:58 PM   #5
Hiroki
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Hi maubp,

Thanks a lot
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