Hi guys,
I ve 76bp long RNAseq single end reads. I ve used Tophat to align these reads onto human genome sequence. After aligning the reads, I browsed the alignment file using samtools tview. As the reads are single end, they should align with the reference genome only in forward direction. Most of the reads are in forwad direction. But there are many lowercase reads, I suppose they are the reads aligned to the reference in reverse direction.
I am confused what should I do. I think these reads have aligned to the reference in reverse direction due to sequence homology (inverted repeats). I will use the BAM file for SNP calling in my downstream analysis. I m not confident over thse alignments. What should I do? Should I discard them? Is there any tool to discard such reads?
Thanks.
I ve 76bp long RNAseq single end reads. I ve used Tophat to align these reads onto human genome sequence. After aligning the reads, I browsed the alignment file using samtools tview. As the reads are single end, they should align with the reference genome only in forward direction. Most of the reads are in forwad direction. But there are many lowercase reads, I suppose they are the reads aligned to the reference in reverse direction.
I am confused what should I do. I think these reads have aligned to the reference in reverse direction due to sequence homology (inverted repeats). I will use the BAM file for SNP calling in my downstream analysis. I m not confident over thse alignments. What should I do? Should I discard them? Is there any tool to discard such reads?
Thanks.
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