I'm having terrible problems to map/align single end RNA files from human genome (
GRCh.38). It is genomic DNA but was prepared by using a RNA library kit to preserve strand specificity.
I've first tried STAR and Kallisto and the coverage was very very low. Then, I've tried bowtie2 as the experiment is more like ChIP seq and the coverage is still very poor (see output for
41115150 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 102795 + 0 mapped (0.25% : N/A)
Any advice about how to deal with this data? Thank you