CrossMap does not seem to transfer gene and mRNA from GFF file

[pckorhon]

Hi, in multiple occations, CrossMap does not seem to remap gene and mRNA lines from the input GFF file despite transferring exon and CDS lines for that particular gene. Does crossmap understand the gene models in a GFF file, is there any check of correctness of the model and should the program be able to transfer complete gene models including at least exon, mRNA, exon and CDS lines.

[liguowang]

When there is a break (a small gap) in the chain file, it’s possible to see that the whole gene cannot map to the target assembly although each exon can be mapped. This is because crossmap will stop if one block (eg, the gene body from TSS to TES) from the source assembly map to two(or more) discontinuous blocks in the target assembly.

Crossmap does not try to understand the gene model of the GFF or BED file, so we recommend doing this at the exon level.

Hope this helps.

Liguo

On Apr 22, 2020, at 11:03 PM, pckorhon [email protected] wrote:

 Hi, in multiple occations, CrossMap does not seem to remap gene and mRNA lines from the input GFF file despite transferring exon and CDS lines for that particular gene. Does crossmap understand the gene models in a GFF file, is there any check of correctness of the model and should the program be able to transfer complete gene models including at least exon, mRNA, exon and CDS lines.

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[liguowang]

When there is a break (a small gap) in the chain file, it’s possible to see that the whole gene cannot map to the target assembly although each exon can be mapped. This is because crossmap will stop if one block (eg, the gene body from TSS to TES) from the source assembly map to two(or more) discontinuous blocks in the target assembly.

Crossmap does not try to understand the gene model of the GFF or BED file, so we recommend doing this at the exon level.

Hope this helps.

Liguo

On Apr 22, 2020, at 11:03 PM, pckorhon [email protected] wrote:

 Hi, in multiple occations, CrossMap does not seem to remap gene and mRNA lines from the input GFF file despite transferring exon and CDS lines for that particular gene. Does crossmap understand the gene models in a GFF file, is there any check of correctness of the model and should the program be able to transfer complete gene models including at least exon, mRNA, exon and CDS lines.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[liguowang]

When there is a break (a small gap) in the chain file, it’s possible to see that the whole gene cannot map to the target assembly although each exon can be mapped. This is because crossmap will stop if one block (eg, the gene body from TSS to TES) from the source assembly map to two(or more) discontinuous blocks in the target assembly.

Crossmap does not try to understand the gene model of the GFF or BED file, so we recommend doing this at the exon level.

Hope this helps.

Liguo

On Apr 22, 2020, at 11:03 PM, pckorhon [email protected] wrote:

 Hi, in multiple occations, CrossMap does not seem to remap gene and mRNA lines from the input GFF file despite transferring exon and CDS lines for that particular gene. Does crossmap understand the gene models in a GFF file, is there any check of correctness of the model and should the program be able to transfer complete gene models including at least exon, mRNA, exon and CDS lines.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.