Fastx collapsed

[frymor]

Hi all,

I was wondering whether there is a way of working in bowtie with the collapsed data from fastx.

I would like to run bowtie with after screening my paired-end reads for multiple occurrences.

Q1 is it possible to run fastx_collapsed with paired-end data and than bowtie? do the pairs will still match?

Q2 the output of fastx_collapsed is fastA, I would like to have a fastq file with the qualities. Is there a way of keeping it in a fastq form?

Thanks

Assa