I used Bowtie to align CLIP-seq reads to genome with the parameter "-v 1" which allow the reads have one mismatch. But in the result, Bowtie treat all the nucleotides of reads as insertion. For example:
2-42 16 chr11 86397621 255 23M * 0 0 GTCAACATCAGTCTGATAAGCTA IIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:23 NM:i:0
Does any one have any idea what happened? What should I do to make it work?