Tophat paired end alignment help: comma or blank to separate two pairs?

[mediator]

Hi All,
I am using the current command to run a PE alignment in Tophat:
$ tophat -p 4 -m 2 -r 200 /index/hg19 /data/raw/N1_1.fa,N1_2.fa

my question is, both N1_1.fa and N1_2.fa are the paired end reads generated from a single human tissue sample. Should I use comma or blank to separate those two? And here is the log for the alignment, is 76% alignment looks normal? Thanks!

# reads processed: 242980185
# reads with at least one reported alignment: 185782139 (76.46%)
# reads that failed to align: 56208030 (23.13%)
# reads with alignments suppressed due to -m: 990016 (0.41%)
Reported 457696000 alignments to 1 output stream(s)

[jbrwn]

a space between file_1 and file_2.

[mediator]

@jbrwn
Thanks! Hope that improves my alignment rate.

[jbrwn]

@jbrwn
Thanks! Hope that improves my alignment rate.

i typically include --mate-std-dev <int> as well, though i'm not sure how much difference it makes. this information should be available from the bioanalyzer output or someone-from-the-lab output.