What is this format? How to run bowtie on it.

[zack80.liu]

I am a newbie to NGS. Please help.

I have the following file (I was told that it is a export file of illumina)

HWUSI-EAS1744 1 8 1 1165 18707 0 1 CAACAACTCACCTGCCGAACCAACTAGCTCTGACAACCGATGTCAATCGAACATCGGACGCAATGGAGAACAACG BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB NM N
HWUSI-EAS1744 1 8 1 1166 9747 0 1 GGCAAGCCGGATCCGTAACTTCGGGATAAGGATTGGCTCTAAGGGCTGGGTCGGTCGGGCTGGGGCGCGAAGCGG bbbbbbabbbbbbbbbbbbbbbbbabbbbb`_bbbbbbbbbbbbbbbbbba`bb__bbb[W]`^^BBBBBBBBBB 0:0:1 Y

Q1: How do I convert this to fastaq format?
Q2: Is bbbbbbabbbbbbbbbbbbbbbbbabbbbb`_bbbbbbbbbbbbbbbbbba`bb__bbb[W]`^^BBBBBBBBBB the quality score?
Q3: How to run bowtie on this file.

Thanks.

[HSJD19]

Format

This is an export file.
HWUSI-EAS1744181116518700 1 - Unique Read Identifier
CAACAACTCACCTGCCGAACCAACTAGCTCTGACAACCGATGTCAATCGAACATCGGACGCAATGGAGAACAACG - Sequence

BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB - Quality Score in Illumina Platform

N - The Y or N in the last column is from the Illumina CHASITY filter. Y means yes it pass N means no . I don't think you should use the N sequences.

[HSJD19]

Might I also suggest reading this thread

http://seqanswers.com/forums/showthread.php?t=4589

[zack80.liu]

Thanks for the reply.