I have a set of RNA-seq dataset of single end 100bp reads (30 million per sample), and first using tophat2, mapping rate is only 5% to the ref genome. Then I tried to trim raw data to 40-100bp, and mapping rate increase to 18%. I'm doing the mapping with no trimmed data right now...
I wonder what other ways I can try to increase the mapping rate? trim read range to 50-100? increase the phred score based on fastqc?
Any comments will be appreciated!
I wonder what other ways I can try to increase the mapping rate? trim read range to 50-100? increase the phred score based on fastqc?
Any comments will be appreciated!
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