psiPerEvent problem

[zjanna]

Dear Eduardo,
I have a problem using Suppa2 because at the end I get matrices with NA and messages: ERROR:psiCalculator:PSI not calculated for event...
for SALMON mapping I use the Homo_sapiens.GRCh38.cdna.all.fa.gz file, while in the SUPPA program to generateEvents I use Homo_sapiens.GRCh38.109.gtf....Could you suggest which fasta file to use here to get the transcripts count matrix and later which and which gtf file to use in SUPPA?
Best regards, Joanna

[EduEyras]

Hi Joanna, It will be partly solved if you use the same annotation for the fasta and for the GTF It could be that there are many transcripts with zero reads, which will also lead to NAs You can also modify the number of NAs allowed. I hope this helps Eduardo

On Wed, 31 May 2023 at 18:12, zjanna ***@***.***> wrote: Dear Eduardo, I have a problem using Suppa2 because at the end I get matrices with NA and messages: ERROR:psiCalculator:PSI not calculated for event... for SALMON mapping I use the Homo_sapiens.GRCh38.cdna.all.fa.gz file, while in the SUPPA program to generateEvents I use Homo_sapiens.GRCh38.109.gtf....Could you suggest which fasta file and which gtf file to use here to get the transcripts count matrix? Best regards, Joanna — Reply to this email directly, view it on GitHub <#164>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB5SXBXSJHJ47BNM5ILXI4KRHANCNFSM6AAAAAAYVHIKHI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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