SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   Combine pairend reads into one file for SOPRA (http://seqanswers.com/forums/showthread.php?t=23412)

Hiroki 09-17-2012 08:18 PM

Combine pairend reads into one file for SOPRA
 
Hi there,

Sorry for a pitifully newbie question:confused:.

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

themerlin 09-17-2012 09:42 PM

Try either shuffleSequences_fastq.pl included with Velvet or this:

http://www.ngcrawford.com/2012/03/28...red-end-reads/

Hiroki 09-18-2012 12:40 AM

Hi themerlin,

Thanx a lot.
I will try it.

Best,

Hiroki

maubp 09-18-2012 01:37 AM

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.

Hiroki 09-26-2012 08:58 PM

Hi maubp,

Thanks a lot:)


All times are GMT -8. The time now is 12:22 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.