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LuyiTian / scPipe

a pipeline for single cell RNA-seq data analysis
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transcript ID not found #123

Open AmaliT opened 5 years ago

AmaliT commented 5 years ago

Hi, we are trialling the scpipe pipeline on some single cell data. I am getting the following error at the sc_exon_mapping stage. 

R> sc_exon_mapping(inbam=aligned_bam,
+                 outbam=mapped_bam,
+                 annofn=c(exon_annotation),
+                 bc_len = 16, UMI_len = 10, nthreads = 8) 
Error: object 'transcript_id' not found

The gff file was downloaded from here. We noted that our gff file does not have a transcript tag or transcript_id. Is there a way around making sc_exon_mapping working in this case? Thanks in advance

LuyiTian commented 4 years ago

sorry for late reply. you can use dataframe as input for annofn parameter. as we mentioned in the help page: data.frame in SAF format or GRanges object containing complete gene_id metadata column.