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I also want the corresponding CDS structure, just as we have the exon structure, something like:
"cds_structure": "89621708,89622244",
We were computing this as (first exon starting position) + (tl_start_site) and (last exon ending position + tl_stop_site) or opposite as in this case, the given that this transcript is on the reverse strand: 89623194 - 951 = 89,622,243 + 1 so the beginning of our CDS structure is: "cds_structure": "89621708,89622244",
The problem we hit doing it this way is that it doesn't account for partially aligning exons. Is there a straightforward way to grab this CDS structure information using the library that will take this into consideration? One out of the box idea I had was checking for the genomic position of C.1 (and C.*1 -1 ). This would at least get the start and stop correct but I'm not sure about all of the other positions.
Thanks!
The text was updated successfully, but these errors were encountered:
HGVS provides the following transcript information:
Example transcript: NM_001126049.1
"exon_structure": "89618918,89623194",
"relative structure": "[[1, 4277]]",
"tl_start_site": 951,
"tl_stop_site": 1487
I also want the corresponding CDS structure, just as we have the exon structure, something like:
"cds_structure": "89621708,89622244",
We were computing this as (first exon starting position) + (tl_start_site) and (last exon ending position + tl_stop_site) or opposite as in this case, the given that this transcript is on the reverse strand: 89623194 - 951 = 89,622,243 + 1 so the beginning of our CDS structure is: "cds_structure": "89621708,89622244",
The problem we hit doing it this way is that it doesn't account for partially aligning exons. Is there a straightforward way to grab this CDS structure information using the library that will take this into consideration? One out of the box idea I had was checking for the genomic position of C.1 (and C.*1 -1 ). This would at least get the start and stop correct but I'm not sure about all of the other positions.
Thanks!
The text was updated successfully, but these errors were encountered: