Hi,
How can I merge two paired end fastq (R and L) to give a single fastq file ?
Thanks,
N.
How can I merge two paired end fastq (R and L) to give a single fastq file ?
Thanks,
N.
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Last edited by NicoBxl; 10-13-2011, 01:41 AM. -
For example here's two paired reads :
Code:@HWUSI-EAS529:41:FC62YHFAAXX:8:1:7969:1330 1:N:0:GCCAAT CTACGAAAGGGCACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCT + IIIIIIIHIIHIIIIIIHHIIIHGIIIIEIIIIIIEIIHIIIIIIIIIIIHIIIIIBHIHIIHGIGIEGHHEGEEH
I find the adapter in the first one :Code:@HWUSI-EAS529:41:FC62YHFAAXX:8:1:7969:1330 2:N:0:GCCAAT AGTGCCCTTTCGTAGGATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAA + IIIIIIIIIIIIIIIIIIIIIIIDHIGIIIHIIIGHGIIIIIIIHHIHIIIIIIIIIHIIIIIIIIHIIGIIIIHI
but not in the second one ...Code:EMBOSS_001 1 CTACGAAAGGGCACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGC 50 ||||||||||||||||||||| EMBOSS_001 1 ---------------TGGAATTCTCGGGTGCCAAGG-------------- 21 EMBOSS_001 51 CAATATCTCGTATGCCGTCTTCTGCT 76 EMBOSS_001 22 -------------------------- 21 -
The velvet assembler comes with shuffleSequences perl scripts that do that will do that for fasta or fastq files.
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