Hi, I am trying to import salmon quant data to isotypeswitchanalyzeR for transcript variant use analysis. But I am seeing this error-
aSwitchList <- importRdata(
isoformCountMatrix = txi.tx$counts,
isoformRepExpression = txi.tx$abundance,
designMatrix = mycols,
isoformExonAnnoation = "hg19_knowngene.gtf",
showProgress = FALSE
Step 1 of 6: Checking data... Using row.names as 'isoformid' for 'isoformCountMatrix'. If not suitable you must add them manually. Using row.names as 'isoformid' for 'isoformRepExpression'. If not suitable you must add them manually. Step 2 of 6: Obtaining annotation... importing GTF (this may take a while) converting annotated CDSs
Error in importRdata(isoformCountMatrix = txi.tx$counts, isoformRepExpression = txi.tx$abundance, :
The annotation and quantification (count/abundance matrix and isoform annotation) seems to be different (jacard similarity < 0.95).
Either isforoms found in the annotation are not quantifed or vise versa.
78631 isoforms were quantified.
82960 isoforms are annotated.
Only 78631 overlap.
This combination cannot be analyzed since it will cause discrepencies between quantification and annotation thereby skewing all analysis.
Please make sure they belong together and try again. For more info see the FAQ in the vignette.
The GTF file I used during salmon quantification contains 82860 transcripts whereas my quant files contain 78631 rows.
Any help would be appreciated.