User: T_18

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T_1840
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Posts by T_18

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Comment: C: How to get similar naming protein seqs and gff from downloaded genome files
... @genomax And just to add, because it is from various sources the files have there own specific issues. So a simple rewriting solution for one, does not help for the other. Might be the best to simply extract proteins from scratch using the gff file? ...
written 3 months ago by T_1840
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Comment: C: How to get similar naming protein seqs and gff from downloaded genome files
... Unfortunately this is not data of just a single source but it is mixed from various public databases or supplementary datafiles of papers. Thats also why some part of the datafiles are perfectly fine and protein files have similar naming as the GFF but unfortunately for a very large part the names a ...
written 3 months ago by T_1840
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How to get similar naming protein seqs and gff from downloaded genome files
... Hi all, Dear all, I am currently facing an issue for which a student of mine and myself have tried to find a solution (I don’t think we are the only ones with this problem). But we have not found a solution ourselves yet. It might be a good idea to get some advice from the experts: you! For a gen ...
genome bedtools gff unix written 3 months ago by T_1840
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Comment: C: Changing gene headers in .sqn file for genome upload NCBI
... I actually now think to do the gene name replacement on the original GFF file. In that case I am sure that the resulting .sqn is built correctly and I have not accidentally changed anything in the .sqn that shouldn't be changed! ...
written 5 months ago by T_1840
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Comment: C: Changing gene headers in .sqn file for genome upload NCBI
... But what I understood from the NCBI tutorials (but it is quit hard to get everything!) is that this .sqn file is the only file I need to upload and is derived from the assembly and the GFF file. Am I right here? If I still need to upload the GFF file also, than indeed this will not work. ...
written 5 months ago by T_1840
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Comment: C: Changing gene headers in .sqn file for genome upload NCBI
... On your first question, I was afraid of that too. But this .sqn file is the only file I upload so it contains the genome assembly (does not get changed) and the information of the GFF file. Because I do want to edit the gene headers in all occasions within this file I think it should be working out ...
written 5 months ago by T_1840
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Comment: C: Changing gene headers in .sqn file for genome upload NCBI
... Just to add, I have created a text file with in the first column the old gene name and in the second column the new gene name: > augustus_masked-tulip_contig_306_pilon_pilon-processed-gene-0.1-mRNA-1 gene1 > maker-tulip_contig_306_pilon_pilon-augustus-gene-0.12-mRNA-1 gene2 > m ...
written 5 months ago by T_1840 • updated 5 months ago by GenoMax92k
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Changing gene headers in .sqn file for genome upload NCBI
... Dear all, My question might be quit specific but hopefully there is someone that might have some advice for me. I am trying to upload a .sqn file to the NCBI genome database. I received the error that my sequence/gene headers are too long. The headers are automatically generated by the annotation s ...
ncbi .sqn unix written 5 months ago by T_1840
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Comment: C: Extract protein sequences or names based on GFF and protein file
... thanks for your quick reply! I also have several genome files which are not available via Entrez. I guess the best and most efficient would than be to use seqkit/bedtools also to extract the genes based on the original gff file and genome assembly file? There is not a more efficient way where I can ...
written 6 months ago by T_1840
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Extract protein sequences or names based on GFF and protein file
... Dear all, In short, my gene ID's of the gff file do not correspond with the protein headers while I do need this for an analysis. What can I do to make sure the protein headers are identical to the gene ID's in the GFF file? I am doing a genome comparison of circa 40 species, for which I want to d ...
gff unix written 6 months ago by T_1840

Latest awards to T_18

Popular Question 5 months ago, created a question with more than 1,000 views. For Trimming sequences based on NCBI contamination screen report
Popular Question 6 months ago, created a question with more than 1,000 views. For Bulk download of gene names NCBI
Popular Question 19 months ago, created a question with more than 1,000 views. For Python script to remove sequences from a fasta file
Popular Question 22 months ago, created a question with more than 1,000 views. For Bulk download of gene names NCBI
Popular Question 22 months ago, created a question with more than 1,000 views. For Bulk download of gene names NCBI

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