User: Juke-34
Juke-34 • 1.8k
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Posts by Juke-34
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Comment:
C: IGB won't open .gff file.
... She/he said at the top of the page...
> Anguilla rostrata (American eel)
Representative genome: Anguilla rostrata (assembly ASM160608v1)
Download sequences in FASTA format for genome
Download genome annotation in GFF, GenBank format
BLAST against Anguilla rostrata genome
I don’t think she/he ...
written 1 day ago by
Juke-34 • 1.8k
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Comment:
C: IGB won't open .gff file.
... This gff file is completely stupid, never seen that before. It doesn't contain anything interesting, no structural annotation (position of feature like gene, trna, pseudogene, etc). It looks like description of sequences of an assembly. It describes the size of 80 000 sequences.
So it's a gff of an ...
written 1 day ago by
Juke-34 • 1.8k
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90
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Comment:
C: IGB won't open .gff file.
... Could you provide a sample of your gff fille ? Do you load the fasta separately or is it embedded in your gff ? ...
written 1 day ago by
Juke-34 • 1.8k
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168
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Comment:
C: Mapping transcripts to genome
... MAKER use blastx+ exonerate to map the proteins to the genome. ...
written 2 days ago by
Juke-34 • 1.8k
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... In the functional annotation part that I teach I list few tools/approaches that can be of interest for you.
Have a look [here][1] at the slide 25. Note that Trinotate is now automated.
[1]: https://github.com/SGBC/course/blob/master/docs/nbis_annotation/slides/Functional_annotation.pdf?raw=true ...
written 2 days ago by
Juke-34 • 1.8k
1
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2
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152
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... Hi imda,
Yes it does. ...
written 3 days ago by
Juke-34 • 1.8k
1
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152
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... Try both and you will see the difference ;).
The main reason I prefer maker_merge_outputs_from_datastore.pl beside the fact that the result is more complete (It collects all tracks not only the maker annotation, it collects proteins and transcripts too in one go, it backups the .ctl files because we ...
written 5 days ago by
Juke-34 • 1.8k
0
votes
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152
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... They are stop codons. MAKER include stop codon within the CDS.
You could get rid of them by using ‘- -cfs’ option while using the script (stand for: Clean Final Stop). ...
written 5 days ago by
Juke-34 • 1.8k
1
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152
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... Btw as you can run tools from that repo I suggest you use maker_merge_outputs_from_datastore.pl to Merge output from Maker. ...
written 6 days ago by
Juke-34 • 1.8k
0
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... It just means that when you have an mRNA made from 3 exons (multi exons structure are common in eukaryotes), using ‘-t exon’ will not extract the 3 exons independently (as there are 3 exon features in your gff, one by line) but rather recreate the mRNA by concatenating them properly. ...
written 6 days ago by
Juke-34 • 1.8k
Latest awards to Juke-34
Scholar
6 days ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Scholar
12 weeks ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Appreciated
4 months ago,
created a post with more than 5 votes.
For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
Appreciated
4 months ago,
created a post with more than 5 votes.
For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
Appreciated
4 months ago,
created a post with more than 5 votes.
For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
Popular Question
5 months ago,
created a question with more than 1,000 views.
For Bioinformatician in genome annotation, Uppsala, Sweden
Scholar
7 months ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Bioinformatician in genome annotation, Uppsala, Sweden
Good Answer
11 months ago,
created an answer that was upvoted at least 5 times.
For A: Trinity strand specific: RF or FR
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12 months ago,
created a post with more than 5 votes.
For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
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14 months ago,
voted at least 25 times.
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Where is it possible to submit annotated eukaryote genomes?
Scholar
16 months ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: Where is it possible to submit annotated eukaryote genomes?
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: Where is it possible to submit annotated eukaryote genomes?
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17 months ago,
created a comment with at least 3 up-votes.
For C: How to manipulate a gff or gtf file manually?
Guru
17 months ago,
received more than 100 upvotes.
Appreciated
24 months ago,
created a post with more than 5 votes.
For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
Teacher
24 months ago,
created an answer with at least 3 up-votes.
For A: Where is it possible to submit annotated eukaryote genomes?
Popular Question
24 months ago,
created a question with more than 1,000 views.
For Emboss seqret - problem conversion gff+fasta to EMBL
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