Timeline for After running nf-core, is there a way to map a gene_id to a specific gene's DNA sequence?
Current License: CC BY-SA 4.0
16 events
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| Mar 4 at 5:55 | comment | added | user18959 | Got it working now. These gtf files have a lot information that needs to be cleaned / corrected (e.g. missing gene IDs), but it appears to now run! | |
| Mar 4 at 5:54 | vote | accept | user18959 | ||
| Feb 22 at 0:38 | comment | added | user18959 | Yep, just running and testing the pipeline with the updated fasta and gtf files to determine if TP53 is ultimately found with the nf-core pipeline (which I expect it should) — but these new files keep resulting in the pipeline terminating due to an error somewhere in the files which I'm trying to trace down | |
| Feb 21 at 11:07 | comment | added | darked89 | Ok. Still, file another question about the gff to gtf conversion of that particular gff file. And it will be helpful if you up vote and accept the answer as a correct one | |
| Feb 21 at 11:01 | comment | added | user18959 | I think I've found the solution here where the larger repo of files are available | |
| Feb 21 at 10:42 | comment | added | user18959 | It's part of the nf-core pipeline — it expects annotations in GTF format, but the above link only provides GFF files. I tried using gff3_ID_generator.py to generate IDs if the gff file does not have them for every feature, but the error persists | |
| Feb 21 at 10:32 | comment | added | darked89 | re conversion gff to gtf: this is a separate question. BTW, why you need it? | |
| Feb 21 at 10:15 | comment | added | user18959 |
I tried converting the GFF to GTF using this method but keep hitting into: KeyError: 'id-LOC110351722' (perhaps due to "gene_id" key not being present for key-value pairings of the .gtf file) — trying to resolve it, but if you have any thoughts, certainly glad to receive it
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| Feb 21 at 9:58 | comment | added | user18959 | That works great — thank you! Going to test this all out now | |
| Feb 21 at 9:54 | comment | added | darked89 | download the annotation then: ``` zcat GCF_015476345.1_ZJU1.0_genomic.gff.gz | grep "gene=TP53;" | more``` | |
| Feb 21 at 9:40 | comment | added | user18959 | I did find this updated version (from 2023-12-14) of the genome here, but is there any way to confirm that the GFF/GTF file includes TP53? | |
| Feb 20 at 23:25 | comment | added | user18959 | Thank you! For clarity, how did you find that contig? Also, strangely the genome fasta file seems to be corrupted in some way (but other files work, e.g. GTF annotation). Is this genome fasta file hosted anywhere else by chance? | |
| Feb 17 at 16:59 | comment | added | darked89 | Also you may try to align the above contig to probably more complete chicken genome to get an idea about how good is the annotation of the p53 gene in mallard/is there anything missing. | |
| Feb 17 at 16:55 | comment | added | darked89 | It is this contig NW_024009712 you will have to get both the genome fasta ans GTF annotation from ncbi.nlm.nih.gov/datasets/genome/GCF_015476345.1 | |
| Feb 17 at 15:06 | comment | added | user18959 |
Thank you for this insightful response! For the last part, could you add more details about this step of alignment against the genome? Namely, how exactly can I confirm the contig containing the TP53 gene is present and identified using STAR?
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| Feb 16 at 10:45 | history | answered | darked89 | CC BY-SA 4.0 |