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i checked and yes is a stranded protocol. all the reads map on the opposite strand of mRNA. thank you very much!!
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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.
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strange alignment results from RIPseq
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?Last edited by Schelarina; 12-23-2014, 10:22 AM.Tags: None
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