User: Picasa
Picasa • 390
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Posts by Picasa
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C: EBI submission and AGP ?
... Thanks Juke-34.
But that's not practical ? I want to allow user to download the final genome (at scaffold level) and not contigs + agp. ...
written 18 days ago by
Picasa • 390
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... Hi,
Has anybody already submitted a genome in EBI ?
For the scaffold assembly they ask for a fasta file and an AGP file.
see this link: https://ena-docs.readthedocs.io/en/latest/cli_02.html
I just have the fasta (assembly) but how to generate this AGP ?
Thanks a lot. ...
written 19 days ago by
Picasa • 390
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... Oh sorry, I will detail more. 50x or 100x seems quite a lot no ?
I have 7 genes and 200 individual of the same species (but different populations), so a total of 1400 genes to anaylse.
The genes are quite short (500 bp in average).
And my goal is to make a tree of genes.
...
written 8 weeks ago by
Picasa • 390
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... Yes I need a representative sequence for each gene and species but my idea was more like sequencing each gene for each species at a certain coverage (how much, is my question) with high-throughput sequencing and get the "most represented".
Example for one gene of one species, if I have a coverage o ...
written 8 weeks ago by
Picasa • 390
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... Hello,
My goal is to make a gene tree of different genes and multiple species.
I will amplify genes via pcr and get amplicon sequencing.
Do you have any recommendation for the sequencing coverage ?
Thanks. ...
written 8 weeks ago by
Picasa • 390
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... but it is already in bed format no ? ...
written 3 months ago by
Picasa • 390
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... Thanks Pierre, your command was very useful.
I am wondering if you know a way to extract regions of these "comm.bed" but relative to my 3 samples (S1.bam S2.bam S3.bam)
So for instance :
RF01 10 3295
is the coordinates in the reference genome
but I would like the coordinates in my sampl ...
written 3 months ago by
Picasa • 390
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... Thanks but it is not what I am looking for. This thread talks about finding DNA sequences from a primer pair, while I want the reverse (finding primer pair from dna sequence) ...
written 3 months ago by
Picasa • 390
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... Hi Biostars,
I am trying to design primers. For this I have multiple sequences in a fasta file and I have found this program that give kind of nice visualisation:
https://www.ncbi.nlm.nih.gov/tools/primer-blast/
1) However I cannot paste multiples sequences .. Is it normal or I am doing something ...
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... Thanks, but Pierre method is what I was searching for.
Your method output regions where at least 2 samples mapped while I wanted all the samples ...
written 4 months ago by
Picasa • 390
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