Currently if one mate of the read is aligned while the other mate is unaligned, mudskipper treats it as a single-end read. This is not quite right. In the transcriptome bam, also one end should remain unmapped (with proper bit in FLAG set and also * as target).
Currently if one mate of the read is aligned while the other mate is unaligned, mudskipper treats it as a single-end read. This is not quite right. In the transcriptome bam, also one end should remain unmapped (with proper bit in FLAG set and also
*as target).