I am trying to measure the expression values ( in RPKM ) for gencode lncRNA uploaded in your site, using flux capacitor. But it shows RPKM 0.000 for all transcript.Can you please suggest a sample command in details?
I am using following command with no luck, all output RPKM is 0.000
sh flux-capacitor -i myinput.bam -a gencode.v12.annotation.patched_contigs.gtf -o myoutput.txt --threads 2
Here is a sample output:
1 HAVANA transcript 12010 13670 . + . transcript_id "ENST00000450305.2"; locus_id "1:11869-14412W"; gene_id "ENSG00000223972.4"; reads 0.000000; length 632; RPKM 0.000000