From what I read, BWA-mem is one of the best alignment tools (at least for de novo transcriptomes).
However, it seems that summarization tools are not always compatible with the SAM files produced by BWA-mem. I need the raw counts per gene. Which tool would be the best choice to use with BWA-mem?
However, it seems that summarization tools are not always compatible with the SAM files produced by BWA-mem. I need the raw counts per gene. Which tool would be the best choice to use with BWA-mem?