My sequencing data has been generated using the dUTP method, which means that when viewed in IGV or other browsers the reads are shown as being in the opposite strand from which they are generated. This is usually not an issue but now I need to prepare some figures (using the fantastic bioconductor package gviz) where the direction of the reads is the key. The question is, how to reverse the strandness of the alignments in a bam/sam file?
I have been using a combination of bamToBed | awk | bedToBam but I loose the information on split reads, that is, a split read will become multiple reads. There must a more elegant way of doing it but I am missing it.
I have been using a combination of bamToBed | awk | bedToBam but I loose the information on split reads, that is, a split read will become multiple reads. There must a more elegant way of doing it but I am missing it.
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