User: anderspitman

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anderspitman30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
2 weeks, 3 days ago
Joined:
3 years, 2 months ago
Email:
t*********@gmail.com

Posts by anderspitman

<prev • 7 results • page 1 of 1 • next >
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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 17 days ago by anderspitman30
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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 18 days ago by anderspitman30
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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 13 months ago by anderspitman30
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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 2.6 years ago by anderspitman30
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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 2.7 years ago by anderspitman30
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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 2.7 years ago by anderspitman30
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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 2.8 years ago by anderspitman30

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