User: anderspitman

gravatar for anderspitman
anderspitman40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
3 months ago
Joined:
3 years, 5 months ago
Email:
t*********@gmail.com

Posts by anderspitman

<prev • 9 results • page 1 of 1 • next >
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Answer: A: samtools sort by something other than position/name?
... I kinda feel like an idiot right now. Upon further reflection on my task, I realized that in this particular case there's no reason to limit myself to samtools' method of sorting. I can simply convert my two BAM files to SAM (without the headers), then feed them to GNU coreutils sort, then diff them ...
written 3 months ago by anderspitman40
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Comment: C: samtools sort by something other than position/name?
... Now that I understand the problem better, you may actually be right about mappings being important for my application. Read names/sequences might be enough of a guarantee for us, but I'm waiting to hear back on that. ...
written 3 months ago by anderspitman40
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Comment: C: samtools sort by something other than position/name?
... I confirmed that bamHash shows the files as matching. I think my solution for now is to just use that. I'm still a little concerned that I don't know which stage of my pipeline is interleaving the reads. From what I've read I should be accounting for all sources of non-determinism (using single core ...
written 3 months ago by anderspitman40
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samtools sort by something other than position/name?
... I'm trying to automatically compare BAM files being output by bowtie2 (for a continuous integration system). Currently using `bamUtil diff` which works well, except I'm noticing sometimes 2 lines in the BAM file will have the same name/start position, but represent different reads. For whatever reas ...
samtools written 3 months ago by anderspitman40
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Answer: A: What Is Ad (Allelic Depth) In 1000Genomes Vcf?
... From the [GATK forum](http://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it): > **AD and DP : Allele depth and depth of coverage.** > > These are complementary fields that represent two important ways of > thinking about the depth of the ...
written 17 months ago by anderspitman40
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Comment: C: How do I load more than 200 nucleotide EST sequences into fasta files from NCBI
... You can use biopython to access entrez direction: http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc108 ...
written 2.9 years ago by anderspitman40
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Comment: C: Using sequence case to encode intron/exon information
... Can you link to any examples where the convention is explained? ...
written 2.9 years ago by anderspitman40
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Using sequence case to encode intron/exon information
... I've heard that sometimes sequences are stored in files partially lowercase and partially uppercase, with the intent that lower- or upper-case regions indicate introns or exons. Is this a common practice? Are there file formats that explicitly support this type of encoding? Google hasn't yielded an ...
sequence written 2.9 years ago by anderspitman40
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Answer: A: Install Biom format under Windows
... I recommend opening an issue on there github page: https://github.com/biocore/biom-format ...
written 3.0 years ago by anderspitman40

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Scholar 3 months ago, created an answer that has been accepted. For A: samtools sort by something other than position/name?

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