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Recent Replies
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB
by
DBScan
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300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
Answer: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
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10
So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
Comment: Generating a Bed file from a Fasta file
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Pierre Lindenbaum
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there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
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That's great. I will test it and let you know how it goes. Thank you.
Comment: Generating a Bed file from a Fasta file
by
pirku
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I tried running BLAT, but the output looks like this. Seems like none of the sequences were mapped/aligned
match mis- rep. N's Q gap…
Comment: Where to find old version of GATK best practice
by
GenoMax
142k
You could try and look up a snapshot of the page(s) - https://web.archive.org/
Which specific best practice are you referring to?
https:/…
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
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you could run blast or any other aligner to get the coordinate(s) of your fasta on a reference genome.
Answer: Running STRUCTURE from command line
by
Arthur
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If it cans help,
I got the same error message :
There were errors in the input file (listed above). According to
"mainparams" the inp…
Comment: CreateSeuratObject taking very long
by
Nitin Narwade
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I am not sure whether it will speedup the conversion but you can give it a try.
convert your dataframe into a sparse matrix before creatin…
Comment: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
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The timing for your question is excellent. The fix was released yesterday.
Comment: vcf phasing
by
WouterDeCoster
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> I observed that it doesn't phase genotypes labeled as 0/0
How could such a genotype even be phased?
Comment: Super ehancers
by
Oburah
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Well-noted however just wondering what you me by GFF being shorter. Thank you![See the screeshot snap of the gff file][1]
[1]: /media/i…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
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50
I know illumina will only give me high-quality contigs.
the samples which are to be sequenced with Long_Short read sequence will be used as…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
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50
Hi, Thank you for a detailed responce.
Let me add some more informations.
Long-Read is ~75X coverage.
Short-Read is ~100X coverage.
**For…
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