I mapped my RNA-Seq paired end reads with tophat, on flagstat my results shows very less number of reads mapped to total number of reads submitted , i guess when more mismatches allowed we are supposed to get more number of reads , but here my reads were inconsistent when more mismatches allowed .
Am i right that when more mismatches allowed , we are supposed to get more number of alignments , please help me in understanding how this mismatches effects alignments and what would be the possible reasons that am getting less number of reads , here am sending my results in the attachment.
Thanks in advance
Am i right that when more mismatches allowed , we are supposed to get more number of alignments , please help me in understanding how this mismatches effects alignments and what would be the possible reasons that am getting less number of reads , here am sending my results in the attachment.
Thanks in advance
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