I have a question regarding the definition given in the SplitNCigarReads tool.
This tool should generate K+1 reads where K is the number of N Cigars in the mapped read for RNAseq data. However the bam file that is generated by the tool tells me that those reads are not split but rather softclipped after N Cigar as if they were mapped by a mapper that was unaware of splice sites such as BWA.
Here is the look of the bam file
What should I do?
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