User: stacy734

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stacy73420
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Posts by stacy734

<prev • 10 results • page 1 of 1 • next >
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Comment: A: Exporting fasta from SQL
... Thank you very much! ...
written 7 weeks ago by stacy73420
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Exporting fasta from SQL
... 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. ...
fasta format sql written 8 weeks ago by stacy73420
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Comment: A: Alphabetizing fasta sequence
... Thank you all! Stacy ...
written 3 months ago by stacy73420
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Alphabetizing fasta sequence
... 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. ...
fasta bioinformatics written 3 months ago by stacy73420
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Comment: A: Binning Illumina reads by subread?
... Thanks very much! Science marches on... Stacy ...
written 4 months ago by stacy73420
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Binning Illumina reads by subread?
... 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. ...
fasta illumina binning next-gen written 4 months ago by stacy73420
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Does Minia discard singletons?
... 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 ...
minia written 7 months ago by stacy73420 • updated 23 days ago by Rayan Chikhi1.2k
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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 8 months ago by stacy73420
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Question about k-mer genie output
... Hi everyone, I installed k-mer genie and ran it on a 120GB Illumina dataset. I get this output: ______________________ running histogram estimation Extrapolating number of distinct kmers 70000| processing | [-- ...
k-mer kmer kmer genie written 8 months ago by stacy73420
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Minia estimated genome size
... Hi everyone, I'm experimenting with Minia for genome assembly of a eukaryote with a 500 MB genome size. I've had good luck adjusting the parameters to find the optimum, except for one: estimated_genome_size. The manual suggests this: estimated_genome_size And I have added this to the command li ...
genome assembly minia written 9 months ago by stacy73420 • updated 9 months ago by Rayan Chikhi1.2k

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