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?
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?
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