Hi,
I want to try iReckon on my RNA-Seq data, but I haven't succeeded in getting the correct format for the reference and annotation files.
Has anyone tried it?
I tried formatting my genome.fa with Savant, but I could not find how to format a fasta file there. Also, I would like to use an annotation file from Ensembl and not UCSC, but after converting my gtf to bed format it was not accepted by iReckon.
I tried the following comand:
java -Xmx15000M -jar IReckon-1.0.6.jar accepted_hits.bam genome.fa genes.bed -1 reads.fa
Any help will be very much appreciated!
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