Error with the seed (-l) argument in Bowtie

Question

[Chynoki]

Hi, I want to use Bowtie to align reads on a genome in order to look for miRNA. I'm encountering troubles with running it.

Here is my command line

bowtie -q -S -a -l 18 -n 0 -e 80 -m 5 --best --strata /data/Genomes/mm9/bowtie1/mm9 ../cutadapt/mirCE1.cut.fastq mirCE1_bowtie.sam -al reads_alignes_genome.fa

When I run it, I got the following message:

-l/--seedlen arg must be at least 5

Does someone know what is the problem with my command line?

Thanks a lot.

Sebastien

Answer 1

[h.mon]

If I am not mistaken, I see two errors:

-1 ../cutadapt/mirCE1.cut.fastq

--al reads_alignes_genome.fa

So try with

bowtie -q -S -a -l 18 -n 0 -e 80 -m 5 \
  --best --strata /data/Genomes/mm9/bowtie1/mm9 \
  --al reads_alignes_genome.fa \
  -1 ../cutadapt/mirCE1.cut.fastq \
  mirCE1_bowtie.sam

[Chynoki]

Thank you for your answer,

using the -1 argm seems to need a -2 arg with mates files. I got this using the -1 arg:

Error: 1 mate files/sequences were specified with -1, but 0

mate files/sequences were specified with -2. The same number of mate files/ sequences must be specified with -1 and -2.

Using:

-q -S -a -l 18 -n 0 -e 80 -m 5 --best --strata --al reads_alignes_genome.fa /data/Genomes/mm9/bowtie1/mm9 ../cutadapt/mirCE1.cut.fastq

I got the error:

Saw ASCII character 10 but expected 33-based Phred qual.

But ASCII character10 correspond to LF (Line Feed). I do not understand why I got this error.

Do you maybe have an idea?

Using: -q -S -a -l 18 -n 0 -e 80 -m 5 --best --strata --al reads_alignes_genome.fa /data/Genomes/mm9/bowtie1/mm9 ../cutadapt/mirCE1.cut.fastq

Edit: Found the problem with the score, I didn't suppress lines which were completely trimmed by cutadapt