Bowtie Paired End --al/--un file problems

[newtonb1]

Hello,

I have just recently started working with Bowtie and am having problems with outputting the information that I want. I have paired end reads that are in fastq.gz format and I have been trying to use the —al and —un options. The files are created, but there are not data in either of them. Also, the manual suggests that 2 files would be output for each of the used and unused reads (e.g usedreads_1.fq usedreads_2.fq) given that I am working with paired end data.

Here’s what I am trying:
bowtie2 --un UnusedReads.fq --al UsedReads.fq -x reference.fa -1 pairedendFWD.fastq.gz -2 pairedendREV.fastq.gz -S output.sam

Thanks for any help!

[bbm]

what do you mean of usedreads and unusedreads?
I'm learning how to use bowtie2 as well, and deal with single end data.

[newtonb1]

I've sequenced my plant specimens and the data I have received is all kinds of DNA (cpDNA, genomic DNA, mtDNA). I am trying to use bowtie in reference based alignment to find which sequences out of the pool of data I have are cpDNA. So hopefully, when using the --un and --al options, it should output a file of the sequences it could use to align to the reference and a file of the sequences it couldn't use. Because my data is paired end, I think it should output 2 files (1 for each pair) for the used sequences and 2 for the unused sequences. But it is not.