Do I need to specify the introns on the gtf file for cellranger?
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Entering edit mode
15 months ago
bioinfo ▴ 150

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

fasta gtf cellranger scRNAseq • 697 views
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Entering edit mode
15 months ago
GenoMax 144k

With the latest cellranger (v.7.x) intronic reads are automatically included https://support.10xgenomics.com/docs/intron-mode-rec

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Thank you for replying. Just to clarify then I dont need to add something like shown below to the gtf file?

chr1 HAVANA intron 22120411 22120503 . + . gene_id "A"; transcript_id "A"; gene_name "A"; transcript_name "A"; exon_number 8; gene_biotype "protein_coding";

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