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VCCRI / Sierra

Discover differential transcript usage from polyA-captured single cell RNA-seq data
GNU General Public License v3.0
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Error in peak calling #46

Closed idupanloup closed 2 years ago

idupanloup commented 2 years ago

I'm having issues trying to perform peak calling. Here are the error messages I got:

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
1 gene entries to process
There are 0 unfiltered sites and 0 filtered sites
Error in `$<-.data.frame`(`*tmp*`, "polyA_ID", value = "::-:") : 
  replacement has 1 row, data has 0
In addition: Warning message:
In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type stop_codon. This information
  was ignored.

Do you know what can be the problem ? Many thanks for your feedback Best, Isa

rj-patrick commented 2 years ago

Hi Isa,

It looks like the problem may be with your reference/GTF file. The '1 gene entries to process' message indicates that only 1 gene has been found and the error appears to be due to the peak calling subsequently returning no result. Maybe check that the reference file you're using is correct?

Cheers, Ralph

idupanloup commented 2 years ago

Hi Ralph,

Many thanks for your answer: indeed, there is only one gene in my reference and the peak calling returned no result, for one of my samples. Cheers,

Isa