Output Multimapped reads

[Nikelle Petrillo]

Is there a way to get STAR to output multimapped reads into a separate fastq file?

Thanks!

Nikelle 

[Alexander Dobin]

Hi Nikelle,

this cannot be done not directly from STAR. You can do it using Picard SamToFastq:

$ samtools view -h -F0x100 Aligned.out.bam | awk 'substr($1,1,1)=="@" || substr($12,6)+0 > 1 {print}'  > a.sam

$ java -jar SamToFastq.jar I=a.sam F=r1.fq F2=r2.fq 

Cheers

Alex

[Nikelle Petrillo]

Hi Alex, 

Im having a bit of trouble understanding your code. So, first, it skips all the reads marked as not primary alignments?

Thanks, Nikelle

[Alexander Dobin]

Hi Nikelle,

right, samtools view -h -F0x100 only outputs primary alignments, i.e. one alignment per read.

awk 'substr($1,1,1)=="@" || substr($12,6)+0 > 1 outputs either the header lines (start with @), or those that have the 12th field HI:i:N with N>1 . HI:i:N is 12th field by default, but you may change that with --outSAMattributes option.

Cheers

Alex