User: stacy734

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stacy73440
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Posts by stacy734

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Submitting Genemark annotation to Genbank
... 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 ...
genomes genemark genbank written 5 months ago by stacy73440 • updated 3 months ago by Shalu Jhanwar470
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Comment: C: Best processing for finishing Eukaryotic genomes?
... 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 5 months ago by stacy73440
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Comment: C: Best processing for finishing Eukaryotic genomes?
... I was using it for yeast. A small genome for a eukaryote. ...
written 5 months ago by stacy73440
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Comment: C: Best processing for finishing Eukaryotic genomes?
... Thanks Lieven! I appreciate your advice. ...
written 5 months ago by stacy73440
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Best processing for finishing Eukaryotic genomes?
... 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 ...
genome eukaryotic finishing assembly written 5 months ago by stacy73440
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Comment: A: How to split sequence in fasta file based on long runs of Ns?
... Thank you! This is very useful. With appreciation, Stacy ...
written 8 months ago by stacy73440
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How to split sequence in fasta file based on long runs of Ns?
... 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 ...
fasta unix written 8 months ago by stacy73440 • updated 8 months ago by zubenel110
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Answer: A: Process to remove terminal Ns from fasta?
... 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 10 months ago by stacy73440
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Process to remove terminal Ns from fasta?
... 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. ...
fasta written 10 months ago by stacy73440
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Comment: A: Spades has been running for over a week. Normal?
... 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 11 months ago by stacy73440

Latest awards to stacy734

Popular Question 8 months ago, created a question with more than 1,000 views. For Alphabetizing fasta sequence
Popular Question 8 months ago, created a question with more than 1,000 views. For Binning fasta sequences by size?
Popular Question 12 months ago, created a question with more than 1,000 views. For Question about k-mer genie output
Popular Question 16 months ago, created a question with more than 1,000 views. For Exporting fasta from SQL
Popular Question 20 months ago, created a question with more than 1,000 views. For Question about k-mer genie output

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