Filtering and excluding reads

[dawe]

Hi all, I have a list of 150k reads aligned with maq and I would like to exclude those from the fastq file to end up in an unaligned reads fastq file.
Has anybody a quick solution to do this?

Thanks

d

[maubp]

I'd write a quick Python script myself. What format is the list in? Simple text file?

[dawe]

Yes, but I've solved with fgrep, thanks.

[bioinfosm]

maq map -u [unmapped reads]

The -u option lets you define the file name with unmapped reads. You may parse this to get fastq format, as this file contains one line per read with sequence and quality info.

Could be faster than what you mention already..