Mesuring Bowtie quality

[genbio64]

Dear SeqAnswers,
I have been running Bowtie for alignment of Illumina Solexa short reads. Having run Bowtie extensively I have a question about what metrics I can/should use to measure the quality of my Bowtie runs. Is there a set of pre-defined metrics to use to measure the quality of my Bowtie alignments (i.e. filze size, line count, etc)?

Thank you in advance,

[Melissa]

File size or line count to evaluate your alignment?! No.
I guess the best way is to compare it with another software. If you output it in SAM format, u can use Samtools to look at the alignment. This gives u an idea what is the quality of reads mapped. Could be reads with lots of Ns or sequencing error.