User: Owen S.

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Owen S.350
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350
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Oakland CA
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7 months, 3 weeks ago
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Posts by Owen S.

<prev • 21 results • page 1 of 3 • next >
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Comment: C: How Are Human Sex Chromosomes Handled When Mapping Reads?
... @lh3 also made this helpful post somewhat recently (thanks!): http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use ...
written 20 months ago by Owen S.350
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Comment: C: hg19 vs hg38 in two pictures
... Seven Bridges has announced Graph -- see https://www.sevenbridges.com/graph/ -- but of course it's not open source and pricing is not discussed on the website. ...
written 23 months ago by Owen S.350
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Answer: A: Samtools Mpileup And Overlapping Paired-End Reads
... NOTE! This answer from Ashutosh Pandey is now misleading. At least for anyone using samtools >= 1.0 (which was released ~6 months after the answer was posted). Since 1.0 ([released Aug 15, 2014][1]), we have the (somewhat confusingly named) `--ignore-overlaps` option: -x, --ignore-overl ...
written 2.2 years ago by Owen S.350
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Answer: A: eprimer3 and primer3 incompatible still?
... I was also having this problem. I remember this problem when it first popped up 5 years ago or so, and so I am in disbelief to be dealing with this 5 years later on a fresh install of "emboss" package on a new Ubuntu 14.04 box.  I assume the fault is with the package maintainers, and not EMBOSS. A ...
written 4.8 years ago by Owen S.350
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Comment: C: Generate kmer profiles from a bunch of peptide sequences
... Thanks, but my question relates to peptide, not nucleotide, sequences.  (The Biostrings function you suggested only works with nucleotide seqs.)  ...
written 5.5 years ago by Owen S.350
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Generate kmer profiles from a bunch of peptide sequences
... Can anyone recommend a software solution to do this: Input: about 100,000 short peptide sequences -- unaligned -- of varying lengths, but mostly under 20 residues. Output:  amino-acid profiles (e.g. sequence logo map) describing similar over-represented kmers (say, 3-or 4- or 5-mers). I can th ...
sequence hmm epitope written 5.5 years ago by Owen S.350 • updated 5.5 years ago by Sean Davis25k
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Comment: C: Bowtie2, -M Alignment/Reporting Mode
... First, the question was not about unique reads, it was about reporting only a single, unique alignment per read. Second, your statement "a read is unique if it maps to only one place" makes no sense to me. (Are you confusing "read" with "alignment" or "hit"?) Finally, yes, -M was deprecated with ...
written 5.9 years ago by Owen S.350
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Comment: C: Does Biopython Have Something Like Perl'S Bio::Locatableseq To Map Positions To
... Thanks Peter. I didn't know about Coordinating_mapping, but it's not quite what I was looking for. This looks to me like a way of mapping genomic, mRNA, and protein coordinates (using a GenBank "or similar file" as input). I was looking for something that maps positions between sequences in an al ...
written 6.5 years ago by Owen S.350
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Does Biopython Have Something Like Perl'S Bio::Locatableseq To Map Positions To Columns And Back Again
... Hi, In the past I have happily used perl's Bio::LocatableSeq to map positions in one sequence to positions in another. Does biopython's Bio.Align not have similar functionality? Here is what I want. Given the following Align object: from Bio.Alphabet import generic_dna from Bio.Seq import Seq f ...
biopython written 6.5 years ago by Owen S.350 • updated 6.5 years ago by Peter5.8k
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Answer: A: Samtools Library Source Question -- Bam_Lpileup.C Vs Bam_Pileup.C
... I just realized, bam_lpileup calls bam_pileup - and because it doesn't pass along a max_depth setting, it thus uses the depth of 8000 that is hard-coded in bam_pileup.c. For a work-around, I can just change the 8000 that is hard-coded in bam_pileup.c (As if anyone else in the world is having this ...
written 6.7 years ago by Owen S.350

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Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Bowtie2, -M Alignment/Reporting Mode
Popular Question 19 months ago, created a question with more than 1,000 views. For Tophat / Cufflinks Not Using Gene_Id Or Gene_Name From Gtf File
Great Question 22 months ago, created a question with more than 5,000 views. For Tophat / Cufflinks Not Using Gene_Id Or Gene_Name From Gtf File
Great Question 2.7 years ago, created a question with more than 5,000 views. For Tophat / Cufflinks Not Using Gene_Id Or Gene_Name From Gtf File
Epic Question 2.7 years ago, created a question with more than 10,000 views. For Tophat / Cufflinks Not Using Gene_Id Or Gene_Name From Gtf File
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Generate kmer profiles from a bunch of peptide sequences
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Tophat / Cufflinks Not Using Gene_Id Or Gene_Name From Gtf File
Student 3.8 years ago, asked a question with at least 3 up-votes. For Tophat / Cufflinks Not Using Gene_Id Or Gene_Name From Gtf File
Appreciated 3.8 years ago, created a post with more than 5 votes. For How Fundamental Is The 4 Gb Size Limit For Building Burrows-Wheeler Indices
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Tophat / Cufflinks Not Using Gene_Id Or Gene_Name From Gtf File
Great Question 4.7 years ago, created a question with more than 5,000 views. For Tophat / Cufflinks Not Using Gene_Id Or Gene_Name From Gtf File
Supporter 4.8 years ago, voted at least 25 times.
Appreciated 5.9 years ago, created a post with more than 5 votes. For How Fundamental Is The 4 Gb Size Limit For Building Burrows-Wheeler Indices
Good Question 5.9 years ago, asked a question that was upvoted at least 5 times. For How Fundamental Is The 4 Gb Size Limit For Building Burrows-Wheeler Indices
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Tophat / Cufflinks Not Using Gene_Id Or Gene_Name From Gtf File
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Map Genbank Gi To Accession Numbers (A Million Times)
Popular Question 5.9 years ago, created a question with more than 1,000 views. For How Fundamental Is The 4 Gb Size Limit For Building Burrows-Wheeler Indices
Commentator 5.9 years ago, created a comment with at least 3 up-votes. For C: How Fundamental Is The 4 Gb Size Limit For Building Burrows-Wheeler Indices
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: Bowtie2, -M Alignment/Reporting Mode
Student 5.9 years ago, asked a question with at least 3 up-votes. For Map Genbank Gi To Accession Numbers (A Million Times)
Student 5.9 years ago, asked a question with at least 3 up-votes. For How Fundamental Is The 4 Gb Size Limit For Building Burrows-Wheeler Indices

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