User: Picasa

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Picasa480
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Posts by Picasa

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SnpEff database with maker annotation format
... Hello, I am trying to use SnpEff but I got a non model organism. I am trying now to build the database but my annotation is a Maker GFF format, and I got some issues Anybody have experience with converting the maker GFF format to an other compatible one ) (ex: to GTF) Thanks for your help. ...
snpeff maker written 5 days ago by Picasa480 • updated 5 days ago by prince2612199160
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Comment: C: Extract genes from GTF with variants from VCF
... So basically I had wgs data that I used to call variants (SNPs and indels) -> at the end .vcf file. I have a reference genome fasta file and want to create an alternative genome fasta file (with SNPs and indels) -> This is easy. But the difficulty is that I want to extract transcripts (so I ...
written 25 days ago by Picasa480
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Comment: C: Extract genes from GTF with variants from VCF
... Yes exactly, sorry for not being clear. It's easy to integrate the alternative SNPs (haplotype 2) because it doesn't shift the coordinates of my transcripts (in the GTF), but for indels... I don't have any solutions. ...
written 26 days ago by Picasa480
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Extract genes from GTF with variants from VCF
... Hi, I am studying allele specific expression and I am stuck on the step to get 2 transcripts (one from haplotype 1 and one from haplotype 2). To get genes/transcripts from a GTF I use `cufflink gffreads`: this is not a problem. Now I want to make version 2 (ie. haplotype 2, or alternative) of the ...
gtf variants written 26 days ago by Picasa480
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Comment: C: Get counts for allele specific expression analysis
... Thanks for your link. Do you have experience with ASE study ? ...
written 7 weeks ago by Picasa480
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Get counts for allele specific expression analysis
... Hi all, I am looking for your help about tools/pipeline for allele specific expression analysis. From various papers, I have come up with this pipeline: 1) Call variant with GATK using WGS samples 2) Create 2 transcriptomes using these variants and my annotation: so I have one transcriptome for ...
allele expression ase-tigar rna-seq written 7 weeks ago by Picasa480
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Comment: C: Scaffolding a genome with long reads.
... Thanks I will take a look ...
written 8 weeks ago by Picasa480
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Scaffolding a genome with long reads.
... Hello, I have old illumina genomes that I would like to improve with a scaffolding step. For scaffolding I have long reads (pacbio or nanopore depending on species). Do you have any softwares recommendation to do that ? Thank you. ...
assembly long reads pacbio written 8 weeks ago by Picasa480 • updated 8 weeks ago by lieven.sterck6.4k
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Comment: C: Good coverage value for de novo assembly with NanoPore Reads?
... Hi, > For de novo I would suggest 30-40X, whereby the longest reads are the > most important. Do you have a source for this ? thanks. ...
written 3 months ago by Picasa480
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Comment: C: Location of centromere
... Thanks for the papers ! , I will take a look. ...
written 4 months ago by Picasa480

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