Solexa mapping - extraction of "not in Ref" reads

[Oxygen81]

Hi everyone,

I am searching for a tool/software with which it is possible to map Solexa reads against a reference and which saves the not used reads, too (that's the important part). Is that possible with MAQ?

Thanks for your help
Janina

[Matthias]

Hi,

this is possible with bowtie '--un unaligned_reads.fastq'

[NextGenSeq]

CLC Bio's Genomic Workbench does this.

[maximilianh]

use maq or bowtie and then pipe their sam output into samtools -f4 - > output.sam

will keep only the unmapped reads.

[silin284]

"bowtie --un filename.xxx" will save the unmapped read to a specific file

[bioinfosm]

maq map -u unmapped_readsFile.txt ...

gives you the unmapped reads as well

[Oxygen81]

Hi,

thanks for your help so far! Tried the whole day to understand the SAMtool hint but unfortunately I was not successful. I will describe what I did and maybe someone could help me.

1: mapping of reads against a reference (Maq)
2: conversion of Maq output *.map -> *.sam (maq2sam-long)
3: Sam -> Bam (samtools)
4: sorted bam file with (samtools)
5: ./samtools view -f 12 *.sorted bam *.12.bam

The last step (5) didn't work anymore. It gives no error message but a file with 0 kb (but I know that some reads are not used). I also tried the command with > *.12.bam but nothing happens.
Has someone an idea? I also tried -f 4 and -f 8 but it is the same... At the end I want to have a fastq file.