User: stacy734
stacy734 • 40
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Posts by stacy734
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... 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 ...
written 6 weeks ago by
stacy734 • 40
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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
stacy734 • 40
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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
stacy734 • 40
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... 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 ...
written 3 months ago by
stacy734 • 40
• updated
3 months ago by
WouterDeCoster ♦ 40k
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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
stacy734 • 40
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... 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 ...
written 6 months ago by
stacy734 • 40
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... Thanks finswimmer.
Sadly, that didn't seem to solve the problem. ...
written 9 months ago by
stacy734 • 40
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... 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+$ ...
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... Hi Alex
Thank you for the very clear explanation, and for taking the time!
Stacy ...
written 14 months ago by
stacy734 • 40
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... 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 ...
written 14 months ago by
stacy734 • 40
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For Question about k-mer genie output
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