Dear Kissplice users,
after running kissplice2reftranscriptome
kissplice2reftranscriptome -b assemblychec095n10_okay_okalt_newnames.fasta.transdecoder.bed results_mDr1_EcoC_mDr2_EcoC_mDr3_EcoC_WW1_EcoC_WW2_EcoC_WW3_EcoC_k25_coherents_type_0a.fa -t out_blat_SNP_on_transcripts_80.psl -s kissDE_output_C_pvalue05
and reading the mainOutput[timestamp].tsv file, somenthing is not clear for me.
As reported in the UserGuide, in the columns Codon_1 and Codon_2 should be reported
the SNP(s) from the upper and lower paths respectively. However, the codons reported in both columns (Codon_1 & Codon_2) are the same. This happen for all the SNPs; is this normal?
Thanks in advance for your time,