What is the read file format Maq recognizes?
Reads should be prepared in the standard FASTQ format. • Will SolexaPipeline generate the FASTQ file Maq needs? If not, what should I do? The Gerald module of the SolexaPipeline generates a FASTQ-like format, but it is not a FASTQ in fact. You should convert the format with “maq sol2sanger”. This page gives more explanation. The latest SolexaPipeline-0.3.0 generates a new file in the “Export” format. Read sequences, qualities and most of alignment information is stored in this file. Maq also provides a Perl script to convert various formats to Sanger’s FASTQ format. • My collaborator gave me a read file far from FASTQ. What should I do? First, you should understand what your file means, and then convert your file to the standard FASTQ format. This page may help, too. If you still have difficulty to identify the format, feel free to send an email to the maq-help mailing list, or directly contact with me.
