User: stacy734
stacy734 • 40
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Posts by stacy734
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... Hi all,
I have Genmark-ES output for a plant genome. Genemark output is in gft format and I'm stumped as to how to get it into a format I can submit to Genbank.
Genbank's tbl2asn program requires tbl format annotation.
Various programs (GAG, etc) to convert gft to tbl don't seem to work very well ...
written 6 weeks ago by
stacy734 • 40
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... Improving the assembly as much as possible. Making new joins, allowing manual review of joins and trimming junky stuff. I still expect a draft genome at the end, maybe just a better one. ...
written 7 weeks ago by
stacy734 • 40
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... I was using it for yeast. A small genome for a eukaryote. ...
written 7 weeks ago by
stacy734 • 40
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... Thanks Lieven!
I appreciate your advice. ...
written 7 weeks ago by
stacy734 • 40
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... Hi all,
I am assembling some eukaryotic genomes, and trying different methods for finishing.
I normally start with Spades, followed by a manual contig alignment and additional joins.
Does anyone have a favorite program for genome finishing? It doesn't need to be free. I have tried CLC workbench bu ...
written 7 weeks ago by
stacy734 • 40
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... Thank you!
This is very useful.
With appreciation,
Stacy ...
written 4 months ago by
stacy734 • 40
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... Hi all,
I have a fasta file with some long runs of Ns. I would like to split the sequences with strings of 100 Ns or longer by replacing these strings with a header: >some_string
It isn't necessary to have the header strings be unique, I can renumber the headers afterwards.
One issue: the fast ...
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... Thank you everyone.
This request was to help with submission of genome assemblies to Genbank. They ask that the terminal Ns (gaps) be removed from the ends of contigs. However, I have found that if you simply leave them on they will remove them as part of their process. ...
written 6 months ago by
stacy734 • 40
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... Can anyone recommend a tool or unix command line to remove terminal (leading or trailing) Ns from a fasta file?
Thanks in advance for any advice. ...
written 6 months ago by
stacy734 • 40
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... I have Spades running on a compute farm with 500G RAM. It is still running and only using 310G of the RAM allowed.
There is plenty of disk space (~4 TB).
I'll just let it roll.
Thanks for your comments! ...
written 8 months ago by
stacy734 • 40
Latest awards to stacy734
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created a question with more than 1,000 views.
For Alphabetizing fasta sequence
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For Binning fasta sequences by size?
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For Exporting fasta from SQL
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For Question about k-mer genie output
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