what is wrong with my bowtie2?

[wmseq]

Hi every one,
I don't know why I could not run the following command to align my seqencing data to the reference genome.

bowtie2 -p 8 -f -x hg19 -u ~/my_rnaseq_dat/untreated1.fa -S untreated.sam.

on the contrary, I can run the following command. put the option of -f before the input file instead of -u option.

bowtie2 -p 8 -x hg19 -f ~/my_rnaseq_dat/untreated1.fa -S untreated.sam.

Thanks a lot!

Richard

[winsettz]

Pretty sure it's supposed to be U. I thought flags are case sensitive.

-u/--upto <int> stop after first <int> reads/pairs (no limit)

bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]

<bt2-idx> Index filename prefix (minus trailing .X.bt2).
NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
<m1> Files with #1 mates, paired with files in <m2>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<m2> Files with #2 mates, paired with files in <m1>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<r> Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).

[wmseq]

Thanks for your quick answer!
The problem is that it is still there, after I changed it to capital U.
The error message is as follows:
Encountered internal Bowtie 2 exception (#1)

[winsettz]

This /should/ work. Post the rest of the error message.

bowtie2 -p 8 -x hg19 -f -U ~/my_rnaseq_dat/untreated1.fa -S untreated.sam