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

    Leave a comment:


  • dpryan
    replied
    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.

    Leave a comment:


  • Schelarina
    started a topic strange alignment results from RIPseq

    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.

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