bowtie error

[jamal]

hi all,

I am trying to use Bowtie to align paired end sequencing data from solexa, I made indexfiles, and run bowtie for my files by this command:

bowtie -S -a -v 3 -q -I 0 - X 400 -t /mgs/.../Assembled_chromosomes/renames/Allchro -1 /mgs/.../Sequences_original_08-09/s_1_1_sequence.txt -2 /mgs/.../Sequences_original_08-09/s_1_2_sequence.txt s_1_bowt.sam

read length=101, size of fragment=400bp

but I am consistently getting this:

Extra parameter(s) specified: "400", "/mgs/....../renames/Allchro", "s_1_seq_pe_bowt_101_3mis.sam"
Note that if <mates> files are specified using -1/-2, a <singles> file cannot
also be specified. Please run bowtie separately for mates and singles.
Overall time: 00:00:00

Does anyone have any ideas as to what I should do?

[VIB_user]

i used bowtie
and all i used in my query was a .txt file (that was fastq result) and then the indexes that i downloaded from the site

bowtie -S mm9 ../100920_s_1_seq_GLJ-1.txt mm9_snp_1_1.sam

like this
were -S specifice that i use samtools and mm9 = my indexfiles and the txt file is my fastq file and the .sam = output

[Ben Langmead]

hi all,

bowtie -S -a -v 3 -q -I 0 - X 400 -t /mgs/.../Assembled_chromosomes/renames/Allchro -1 /mgs/.../Sequences_original_08-09/s_1_1_sequence.txt -2 /mgs/.../Sequences_original_08-09/s_1_2_sequence.txt s_1_bowt.sam

Extra parameter(s) specified: "400",

Hi Jamal,

Looks like there's a space between "-" and "X" in the "- X 400" part of your command. If you remove the space ("-X 400"), I think the command should work.

Thanks,
Ben

[jamal]

Hi Jamal,

Looks like there's a space between "-" and "X" in the "- X 400" part of your command. If you remove the space ("-X 400"), I think the command should work.

Thanks,
Ben

Thank you Ben.
I also put my index in current directory , and it worked.
thanks again.