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

[GenoMax]

The -u option is expecting you to provide a number.

-u/--qupto <int>

Align the first <int> reads or read pairs from the input (after the -s/--skip reads or pairs have been skipped), then stop. Default: no limit.

Based on recollection from a past thread, bowtie is sensitive to command line options and expects them to be in a certain order.

[dpryan]

Try -U rather than -u