I"m a new to Galaxy.
I’m trying to analyze my RNA seq data from mice using HISAT2 (or STAR) and featureCount.
My data are stranded paired end.
I could get a good mapping rate in HISAT2, but only 30% of reads were assigned in featureCounts.
HISAT2 (with default settings except for strandedness, R)
I’m using built-in file of mm10 as a reference genome, because I have no idea which FASTQ/GFF3 files I should chose in UCSC/ensemble.
I have also tried STAR without a GFF3 annotation file and faced with the same problem in the counting step by featureCounts. With a GFF3 file I downloaded from ensemble, I couldn’t get results due to an error.
Could you suggest any possible solutions?
I have been in stuck in the same place for a few weeks.
Thank you very much in advance.