User: stacy734

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stacy73440
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Posts by stacy734

<prev • 22 results • page 1 of 3 • next >
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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 6 weeks 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 3 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 3 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 3 months ago by stacy73440 • updated 3 months ago by WouterDeCoster40k
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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 6 months ago by stacy73440
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Advice on Blast output
... Hi everyone, I am running blastn on the commandline, trying different options for formatting. This command: blastn -query blastme.fasta -out remote.blastn -db nr -evalue 1e-30 -outfmt 18 -max_target_seqs=1 & Gives output that looks like this: _________________________________ Accession ...
format unix blast written 6 months ago by stacy73440
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Comment: A: Proper sed format to remove and of line characters?
... Thanks finswimmer. Sadly, that didn't seem to solve the problem. ...
written 9 months ago by stacy73440
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Proper sed format to remove and of line characters?
... Hi everyone, I have a fasta file with some junk at the end of many lines, which I would like to remove using sed. I have tried these formats, but am getting errors inre illegal variable names: sed -e "s/NNG$//g" sed -e "s/NNG\$//g" sed -e "s/NNG$//g" sed -e "s/NNG+$ ...
fasta sed written 9 months ago by stacy73440 • updated 9 months ago by jcabraham0
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Answer: A: Probability of sequence with mismatches
... Hi Alex Thank you for the very clear explanation, and for taking the time! Stacy ...
written 14 months ago by stacy73440
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Probability of sequence with mismatches
... Hi all, I'm drawing a blank as to how to calculate the probability of a sequence of length N with some number of mismatches. For example, a specific 50-mer will occur once in 4^50 ( or 1.267 E 30). (ignoring reverse compliments for this example for clarity.) What would it be if one mismatch were ...
probability mismatches written 14 months ago by stacy73440

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Popular Question 6 months ago, created a question with more than 1,000 views. For Question about k-mer genie output

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