User: stacy734

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stacy73440
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3 years, 2 months ago
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Posts by stacy734

<prev • 27 results • page 1 of 3 • next >
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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 9 weeks 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 9 weeks 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 3 months ago by stacy73440
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Spades has been running for over a week. Normal?
... Hi all, I am running a genome assembly using Spades on a 1GB genome using ~120GB paired-end Illumina reads. The process has been running for more than a week, mostly on the K-mer counting step. The log shows a notation : "Collecting K-mer information, this takes a while" so maybe this is expecte ...
genome assembly spades written 3 months ago by stacy73440
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Does SPAdes assembler lose singlets?
... Hi all, Does anyone know if the SPAdes assembler loses singlets (unassembled strings)? In other words, if it is run on partially assembled deduped genome, will it lose all contigs that can't be further joined? Thanks for any advice. ...
assembly spades genomes written 5 months ago by stacy73440
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Running Genbank check prior to submission?
... Hi everyone, I recently submitted an insect genome to Genbank, and received back a very helpful report showing some contigs had contaminating bacteria. Most of this was removed prior to submission by Blasting against the bacterial db, but it looks like some were missed. Does anyone know how to ge ...
contamination genbank written 7 months ago by stacy73440
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Comment: C: Oxford Nanopore error rate?
... Thank you WouterDeCoster for posting this image. Can you post the title of the paper? I'd like to read it for more details. ...
written 9 months ago by stacy73440
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Comment: C: Oxford Nanopore error rate?
... No, sadly there is no reference genome available. This would be for de novo assembly. ...
written 9 months ago by stacy73440
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Oxford Nanopore error rate?
... I'm considering trying the Oxford Nanopore sequencer. I know at one point they had a very high error rate, which they advertise as being much lower now. I'm looking for a recent paper from an unbiased source that has tested what the error rate is in a real world process. I have emailed the compa ...
rate nanopore oxford error written 9 months ago by stacy73440 • updated 9 months ago by WouterDeCoster43k
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Answer: A: Advice on Blast output
... Thanks! For others who may read this, the parameter in question can either be sskingdom or sblastname. Stacy ...
written 12 months ago by stacy73440

Latest awards to stacy734

Popular Question 4 months ago, created a question with more than 1,000 views. For Question about k-mer genie output
Popular Question 7 months ago, created a question with more than 1,000 views. For Exporting fasta from SQL
Popular Question 12 months ago, created a question with more than 1,000 views. For Question about k-mer genie output

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