Hello all
I am using a software called MetaSim to generate reads based on given genome sequences. My problem is that the reads i produced are paired-ends in one multifasta file. the paired reads look like the following:
>r1.1 |SOURCES={GI=61252,fw,624-696}|ERRORS={67:A}|SOURCE_1="Human poliovirus 1 Mahoney" (8915ea1a18cb58f4a76d99a56ece2a9018e105bc)
ATTGGCCATCCGGTGAAAGTGAGACTCATTATCTATCTGTTTGCTGGATCCGCTCCATTGAGTGT
GTATACT
>r1.2 |SOURCES={GI=61252,bw,789-861}|ERRORS={}|SOURCE_1="Human poliovirus 1 Mahoney" (8915ea1a18cb58f4a76d99a56ece2a9018e105bc)
GCGTTACTAGCTGAATCTCTATAATAATTAATGGTGGTGTAATTAATGGTAGAACCACCATACGC
TCTATTT
>r2.1 |SOURCES={GI=61252,fw,6323-6395}|ERRORS={}|SOURCE_1="Human poliovirus 1 Mahoney" (8915ea1a18cb58f4a76d99a56ece2a9018e105bc)
CCACCAGTGCTGGCTACCCTTATGTAGCAATGGGAAAGAAGAAGAGAGACATCTTGAACAAACAA
ACCAGAG
>r2.2 |SOURCES={GI=61252,bw,6502-6574}|ERRORS={}|SOURCE_1="Human poliovirus 1 Mahoney" (8915ea1a18cb58f4a76d99a56ece2a9018e105bc)
AGCATATAGGTTCCCAAAAGCCATTCTCATTGCCACTGAGTCATTCAAACTAGAAGCTTCAATTA
ATCTGGA
I want the backward reads in a separated file, and the forward reads in another file. Does anyone have any idea about a perl script or any other tool to separate these two reads into two different files; then i will be able to align them using Bowtie or any other alignment tool.
Many thanks
I am using a software called MetaSim to generate reads based on given genome sequences. My problem is that the reads i produced are paired-ends in one multifasta file. the paired reads look like the following:
>r1.1 |SOURCES={GI=61252,fw,624-696}|ERRORS={67:A}|SOURCE_1="Human poliovirus 1 Mahoney" (8915ea1a18cb58f4a76d99a56ece2a9018e105bc)
ATTGGCCATCCGGTGAAAGTGAGACTCATTATCTATCTGTTTGCTGGATCCGCTCCATTGAGTGT
GTATACT
>r1.2 |SOURCES={GI=61252,bw,789-861}|ERRORS={}|SOURCE_1="Human poliovirus 1 Mahoney" (8915ea1a18cb58f4a76d99a56ece2a9018e105bc)
GCGTTACTAGCTGAATCTCTATAATAATTAATGGTGGTGTAATTAATGGTAGAACCACCATACGC
TCTATTT
>r2.1 |SOURCES={GI=61252,fw,6323-6395}|ERRORS={}|SOURCE_1="Human poliovirus 1 Mahoney" (8915ea1a18cb58f4a76d99a56ece2a9018e105bc)
CCACCAGTGCTGGCTACCCTTATGTAGCAATGGGAAAGAAGAAGAGAGACATCTTGAACAAACAA
ACCAGAG
>r2.2 |SOURCES={GI=61252,bw,6502-6574}|ERRORS={}|SOURCE_1="Human poliovirus 1 Mahoney" (8915ea1a18cb58f4a76d99a56ece2a9018e105bc)
AGCATATAGGTTCCCAAAAGCCATTCTCATTGCCACTGAGTCATTCAAACTAGAAGCTTCAATTA
ATCTGGA
I want the backward reads in a separated file, and the forward reads in another file. Does anyone have any idea about a perl script or any other tool to separate these two reads into two different files; then i will be able to align them using Bowtie or any other alignment tool.
Many thanks
Comment