Do I need to specify the introns on the gtf file for cellranger?
Hello,
I need to make a few changes to the human gtf file that I am using before building a reference and doing the alignment with cellranger.
I made the changes to the exons but I want to make sure that the introns are also used. I was looking at how introns were specified on the gtf file but they are not explicitly specified like the exons. Do I need to specify them or would the cellranger count command using the –include introns would recognize them based on the exons and transcript locations?
For example the portion I changed on the gtf looks like below:
chr1 HAVANA gene 2212000 22121097 . + . gene_id "A"; gene_name "A";
chr1 HAVANA transcript 22120200 22121097 . + . gene_id "A"; transcript_id "A"; gene_name "A"; transcript_name "A";
chr1 HAVANA exon 22120200 22120410 . + . gene_id "A"; transcript_id "A"; gene_name "A"; transcript_name "A"; exon_number 8; gene_biotype "protein_coding";
chr1 HAVANA exon 22120504 22121097 . + . gene_id "A"; transcript_id "A"; gene_name "A"; transcript_name "A"; exon_number 9; gene_biotype "protein_coding"`;
So would the software recognize that the intron has the genomic location 22120411 22120503 based on the coordinates that are already on the gtf file?
Thank you
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