I have encountered a problem after using Tophat. I started off with fasta file of my genome reference and a gff3 file of annotation reference. Nine sets of rnaseq data uploaded in my history. I managed to run TopHat for the first two RNAseq data sets and was able to obtain all results from Tophat. However for 5 datasets, there was a problem with the alignment summary, saying that an error occurred setting the metadata for this dataset. It was suggested to set it manually or retry auto-detection.
For the last two datasets, both alignment summary and insertions data from Tophat had this problem. Do you reckon if there is a problem with the RNAseq data file? If so, will there be a way to repair RNAseq data file? Could you please look into this for me and advice.
Many thanks, Darsha