Hi,
I installed the cgat tool via mamba. I want to create the unique chunks at gene level using
--method=genes-to-unique-chunks
so i copied the code from one of the biostars code.
cgat gtf2gtf --method=genes-to-unique-chunks -I /reference_annotation/GRCh38.86.gtf > output.gtf
But i'm getting this error
self.transcript_id = other.transcript_id File "pysam/libctabixproxies.pyx", line 638, in pysam.libctabixproxies.GTFProxy.__getattr__ KeyError: 'transcript_id'
I supplied the entire GTF file without any filtering. Do i have to filter the specifically before i supply to the cgat?
1 answer
Yes, cgat assumes that the input GTF is valid according to the following specification:
http://mblab.wustl.edu/GTF22.html
This means that the transcript_id field is a manditory attribute.
However, modern ensembl GTFs contain gene lines that do not have a transcript_id. The easiest way to filter these out would be either:
awk '$3!="gene" ' /reference_annotation/GRCh38.86.gtf | cgat gtf2gtf --method=genes-to-unique-chunks -L output.log > output.gtf
or
grep "transcript_id" /reference_annotation/GRCh38.86.gtf | cgat gtf2gtf --method=genes-to-unique-chunks -L output.log > output.gtf
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