User: stacy734
stacy734 • 20
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Posts by stacy734
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Comment:
A: Binning fasta sequences by size?
... Thanks to you both! ...
written 3 months ago by
stacy734 • 20
10
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4
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235
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6 follow
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... Hi everyone,
I have a large fasta file and need to bin it by size: everything 200 nt and up in one file, and everything 199 or smaller in another. I have found some useful scripts that will remove the smaller sequences, but they are discarded and I need to keep them in a separate file.
Can anyone ...
written 3 months ago by
stacy734 • 20
• updated
3 months ago by
Matt Shirley ♦ 8.3k
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1
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420
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Comment:
A: Exporting fasta from SQL
... Thank you very much!
...
written 8 months ago by
stacy734 • 20
0
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... Hi everyone,
I have sequences stored in an SQL database, with the header stored in one field and the sequence (single line) in another.
header1 GACTACGACT...
header2 ATACGATCAT...
I've been exporting sequences as a csv and running another process to put them in proper fasta format. ...
written 8 months ago by
stacy734 • 20
1
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363
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Comment:
A: Alphabetizing fasta sequence
... Thank you all!
Stacy ...
written 10 months ago by
stacy734 • 20
10
votes
3
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363
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5 follow
3
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... Hi everyone,
Can someone suggest a method to sort a fasta file by alphabetical order of the sequence (not the defline)?
Any advice will be appreciated. ...
written 10 months ago by
stacy734 • 20
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348
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1
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... Thanks very much!
Science marches on...
Stacy ...
written 11 months ago by
stacy734 • 20
6
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1
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348
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1
answer
... Hi everyone,
I have a very large file of genomic sequence, and need to bin them by the presence or absence of a specific 20-mer. (Everything with the 20-mer in one file, everything without it in another). I tried using grep but the sequences are multi-line.
Any suggestions will be appreciated.
...
written 11 months ago by
stacy734 • 20
0
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359
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... Hi everyone,
I am working with some Minia assemblies. These were run using the no-length-cutoff parameter.
Normally I discard small contigs, but I like to see what comes out before i do.
My question: when using the no-length-cutoff parameter, does Minia keep everything, even the singletons, read ...
written 14 months ago by
stacy734 • 20
• updated
7 months ago by
Rayan Chikhi • 1.3k
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Comment:
C: Question about k-mer genie output
... Thank you for the sane advice.
I will proceed with multiple assemblies with different k-mers. ...
written 15 months ago by
stacy734 • 20
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