User: Picasa

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Picasa490
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Posts by Picasa

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Comment: C: RepeatMasker overlap and interpretation
... Thanks for your answer, it's more clear. However, sorry but I am not familiar with this output but how did you calculate 1900 bp ? I have looked at the sequences `rnd-1_family-52#DNA/Maverick` and `rnd-1_family-50#Unknown` generated by `RepeatModeler` and their size are `6975 bp` and `1116 bp` re ...
written 9 days ago by Picasa490
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Where to upload protein coding gene annotation ?
... Hi all, I have annotated my genome with the classical combo MAKER + Blast2GO. I am writing now a paper about this genome and this protein coding gene annotation. What is it usually do in term of protein coding gene annotation upload ? Do people upload it in their github or specific database ? Th ...
protein maker written 10 days ago by Picasa490 • updated 9 days ago by Juke-343.7k
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RepeatMasker overlap and interpretation
... Dear all, I have run RepeatMasker and I have this kind of result: *out file SW perc perc perc query position in query matching repeat position in repeat score div. del. ins. sequence begin end (left) repeat class/fami ...
overlap repeat written 15 days ago by Picasa490 • updated 15 days ago by lieven.sterck7.2k
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Contig longer than mitochondrial sequence. Explanation ?
... Hi, I am trying to look for mitochondrial sequence in my genome assembly. I have found a contig which correspond to it but the size is longer than expected (contig: 30 kbp while the mitochondrial sequence should be 16 kbp) I am looking for explanation other than assembly error (I have pacbio data ...
mitochondrial contig written 7 weeks ago by Picasa490 • updated 7 weeks ago by vmicrobio250
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hi-c coverage for scaffolding
... Hey all What is the minimum and optimal coverage for Hi-C data in order to get the best results after scaffolding? Is there a coverage cutoff? Thanks for your help ...
assembly hi c scaffold written 9 weeks ago by Picasa490
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Comment: C: gene set filter/selection for training ab initio annotation tools
... Hi Thanks for your guide ! I am working to get a nice set of gene after my 1st round of maker. In that case, what is `annotation_evidence_based.gff` ? ...
written 3 months ago by Picasa490
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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 3 months ago by Picasa490 • updated 3 months ago by prince2612199170
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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 4 months ago by Picasa490
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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 4 months ago by Picasa490
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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 4 months ago by Picasa490

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