User: Picasa
Picasa • 490
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Posts by Picasa
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0
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... 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
Picasa • 490
3
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1
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... 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 ...
0
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1
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61
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1
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... 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 ...
written 15 days ago by
Picasa • 490
• updated
15 days ago by
lieven.sterck ♦ 7.2k
1
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1
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... 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 ...
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... 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
...
written 9 weeks ago by
Picasa • 490
0
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1
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642
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... 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
Picasa • 490
0
votes
1
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... 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. ...
written 3 months ago by
Picasa • 490
• updated
3 months ago by
prince26121991 • 70
1
vote
0
answers
144
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answers
... 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
Picasa • 490
0
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144
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... 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
Picasa • 490
1
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0
answers
144
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0
answers
... 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 ...
written 4 months ago by
Picasa • 490
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