User: Picasa

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Picasa390
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Posts by Picasa

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Comment: 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 Picasa390
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EBI submission and AGP ?
... 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. ...
ebi agp written 19 days ago by Picasa390
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Comment: C: What coverage is recommended for amplicon sequencing?
... 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 Picasa390
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Comment: C: What coverage is recommended for amplicon sequencing?
... 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 Picasa390
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What coverage is recommended for amplicon sequencing?
... 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. ...
amplicon coverage written 8 weeks ago by Picasa390
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Comment: C: How to extract the same mapped region by multiple samples ?
... but it is already in bed format no ? ...
written 3 months ago by Picasa390
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Comment: C: How to extract the same mapped region by multiple samples ?
... 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 Picasa390
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Comment: C: Primer-blast impossible with multiple sequences ?
... 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 Picasa390
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Primer-blast impossible with multiple sequences ?
... 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 ...
sequences primer-blast written 3 months ago by Picasa390 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: How to extract the same mapped region by multiple samples ?
... 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 Picasa390

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