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Old 01-31-2012, 09:25 AM   #1
mediator
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Default Tophat paired end alignment help: comma or blank to separate two pairs?

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)
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Old 01-31-2012, 09:40 AM   #2
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a space between file_1 and file_2.
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Old 01-31-2012, 09:41 AM   #3
mediator
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@jbrwn
Thanks! Hope that improves my alignment rate.
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Old 01-31-2012, 09:44 AM   #4
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Quote:
Originally Posted by mediator View Post
@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.
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