Concordant, Discordant and multiple alignment
I have been trying to analyze RNA seq data for developing wheat seeds at 21 DAA for three samples. I have generated 6.5 GB of data with approx. 33 million paired reads for each sample. The reads were aligned to reference IWGSC Refseq v1.0 using bowtie 2. The alignment summary file shows 66-73% overall mapping rate, with 19.40% multiple alignments, 3.6% discordant alignments and 61% concordant alignments.
My questions are:
a) Is overall mapping rate of 66-73% acceptable?
b) can i have 19.4% multiple alignments in my data and how can they impact my observations?
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aman.a199 •
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