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A friend tried SUPPA2 for alternate splicing on 28 RNAseq samples using Kallisto and GENCODE v44. Their preprocessed abundance files seem correct, but SUPPA2 skips all lines with errors. Anyone know the exact abundance file format SUPPA2 requires?
A friend tried SUPPA2 for alternate splicing on 28 RNAseq samples using Kallisto and GENCODE v44. Their preprocessed abundance files seem correct, but SUPPA2 skips all lines with errors. Anyone know the exact abundance file format SUPPA2 requires?
SUPPA2 can be complicated. Are those abundance files straight from Kallisto? They have to come with correct transcript IDs matching the GTF. Even one mismatch and it'll skip the whole thing without much warning.
Agree with @X-Man SUPPA2 expects a two-column TSV: transcript ID and TPM value, with no headers. Make sure transcript IDs match those in your .ioe files exactly
The SUPPA2 tool requires that you have transcript IDs listed in the first column and TPM values in the second. Make sure the transcript IDs align perfectly with the GENCODE annotation, including any version numbers. The headers should be labeled as target_id and tpm, and they need to be separated by tabs
Absolutely, sticking to strict formatting and making sure the transcript IDs match precisely is essential, SUPPA2 just won't accept any mismatches or extra headers. A clear, two-column TSV format is definitely the best approach.
