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Old 06-17-2011, 12:48 PM   #1
forget1997
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Default how to combine pair end data into one file

Hi guys,
I am a new comer for this forum.
I just run pair end sequencing on Illumina hiseq 2000 and got two files. I was wondering how can I combine each read and output into a single file.
Thanks!
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Old 06-17-2011, 01:18 PM   #2
ECO
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Search please!
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Old 06-17-2011, 02:19 PM   #3
lewewoo
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Linux: cat or sth...
Samtools, merge bam...
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Old 06-18-2011, 09:27 AM   #4
Simon Anders
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why would you want to do this?
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Old 06-19-2011, 04:46 AM   #5
cedance
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I guess if you want to use hmmSplicer, then you'll have to merge the paired end reads. The software doesn't support separately yet.

You could just use a basic unix command: cat pe1.fq pe2.fq > pe_merged.fq
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Old 06-19-2011, 02:24 PM   #6
boetsie
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Some assemblers also require paired-end reads in one file, like Velvet and SSAKE. You can check their scripts to combine the paired-end reads into a single file with the scripts shufflesequences.pl and makePairedOutput2UNEQUALfiles.pl.
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Old 06-19-2011, 02:45 PM   #7
Apexy
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Hi forget1997,
In an attempt to answer your question, I would imagine your aim is to generate a file to be used by velveth. Should this be the case, there are two sample perl scripts "shuffleSequences_fasta.pl" (FASTA) & "shuffleSequences_fastq.pl" (FASTQ) that come with the velveth pakage. Provide them with your files and create a third file of shuffled sequences. If this is not what you want, try and explain a little more. Do you want to join Read1 & Read2 into one read? Do you want to combine both files (cedance & lewewoo suggest something to do this). A respond to Simon's question would surely bring you help.
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