Convert Maq's out put to fasta/fastq?

[bea]

Hi!

I would like to know whether it's possible to convert Maq's out put (out.aln.txt file, after running maq mapview or the unmapped reads files, by incorporating the u option in maq map) back to a fasta/fastq format so that it can be re-used in Maq/ other assemblers.

Thanks

[ewilbanks]

Not totally sure, but I know that the Vancouver Short Read Analysis Package has a tool for converting Maq to BED (http://vancouvershortr.wiki.sourcefo...t/ConvertToBed) and that Aaron Quinlan's BEDTools have a script for generating BED --> fasta.

Hope that helps! Definitely not the most direct way though for sure. :P

[TylerBackman]

R/BioConductor can do this easily, by importing the MAQ output into an AlignedRead object, creating a ShortReadQ object from that, and then exporting a fastq file.

[weibo.xie]

mapview to fastq:

maq mapview maq_map_file |awk '{print "@"$1"\n"$15"\n+\n"$16}' > fastq_file

mapview to fasta:

maq mapview maq_map_file |awk '{print ">"$1"\n"$15}'> fasta_file

unmapped reads file to fastq

awk '{print "@"$1"\n"$3"\n+\n"$4}' unmapped_reads_file > fastq_file

[bea]

I've tried your suggetions. I'm able to create the fastq files with awk and convert that to bfq format required for MAQ. But running MAQ with the bfq files gives me a error:
Assertion failed: (fp_bfq_l), function ma_match.cc, line 557.
Any suggestions why this might happen?

[BENM]

If your fastq name is too long, >35 characters, Maq will delete the front exceed characters, so at this situation, you can't get the actual primary fastq back.
And the primary fastq paired-end reads, every reads in pe1.fastq file should be corresponding to the same line of pe2.fastq file, so you should sort the name of reads in mapview file at first.