strange alignment results from RIPseq

[Schelarina]

Hello,
I did RIP-seq and used bwa to align the reads following this script

bwa index genome.fasta
bwa aln -n 0 file.sai genome.fasta file.fastq
bwa samse file.sam genome.fasta file.sai file.fastq
samtools view -bt genome.fasta -o file.bam file.sam
samtools sort file.bam filesort.bam
samtools index filesort.bam

Strangely enough, I can see that all the reads map antisense to the coding sequence.. How is that possible? where is the mistake? is in the alignment or in the sequencing?

[dpryan]

If it's a stranded protocol then that's normal. The most common library type uses a dUTP-based method such that read #1 maps to the strand opposite of the one from which it arose.

[Schelarina]

i checked and yes is a stranded protocol. all the reads map on the opposite strand of mRNA. thank you very much!!