bowtie2 unmapped reads

[cookiemic]

Hi everybody,

I have used bowtie2 with the -un parameters to get the unmapped reads to a fastq file:

bowtie2 -x phiX -p 10 -N 1 -L 10 -1 read1.fastq -2 read2.fastq --un ./unmapped.fq --al ./mapped.fq

bowtie2 -x phiX -p 10 -N 1 -L 10 -1 read1.fastq -2 read2.fastq --un unmapped.fq --al mapped.fq

Both command give an empty output.
Anyone knows why?

[cookiemic]

I'm using bowtie2 v2.1.0

[Kennels]

You are aligning paired end reads, so I think you need to specify the parameters --un-conc and --al-conc . Check here just in case:
http://bowtie-bio.sourceforge.net/bo...output-options

[cookiemic]

Solved.
Many thanks!

[bandana]

I am using the above mention commands that is:
bowtie2 -x phiX -p 10 -N 1 -L 10 -1 read1.fastq -2 read2.fastq --un-conc ./unmapped.fq --al-conc ./mapped.fq
For my case bowtie is running continuous and the number of reads I am getting is larger than the actual size.Can you please help me with this?

[mastal]

The number of lines in the bam output may be greater than the number of input reads because you get one line for each alignment.