Moderator: Dan D

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Dan D6.5k
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Tennessee
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http://automationdan.com/
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Docendo discimus.

Posts by Dan D

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Job: Work with me at HudsonAlpha Institute for Biotechnology in Huntsville, AL
... If you want to swim in a bottomless sea of sequencing data and have access to a wide variety of interesting projects in the bioinformatics/big data/data science space, this is for you. You'll be working with me on a growing team solving a number of fun challenges with lots of freedom to utilize new ...
job written 6 weeks ago by Dan D6.5k
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Comment: C: Marketing Project Manager
... Hello Sheila.Smaw! We believe that this post does not fit the main topic of this site. This is not related to bioinformatics For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why ...
written 9 weeks ago by Dan D6.5k
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Comment: C: Associate Office Manager, Qiagen, Cary, NC, USA
... Hello Sheila.Smaw! We believe that this post does not fit the main topic of this site. This position is not bioinformatics-related. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell ...
written 10 weeks ago by Dan D6.5k
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Comment: C: Is there any precedent for considering marked duplicates when calculating covera
... OK, I ran it and with the default of mismatch of two it found dup rates between 38-42% on a set of four paired-end datasets. After thinking on this for a bit I come back to my core premise: it's entirely possible that these are not duplicates because of the hundreds of millions of input reads and th ...
written 10 weeks ago by Dan D6.5k
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Comment: C: Is there any precedent for considering marked duplicates when calculating covera
... Oh, right, I didn't address that in my reply. I will give it a try right now. ...
written 10 weeks ago by Dan D6.5k
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Comment: C: Is there any precedent for considering marked duplicates when calculating covera
... @finswimmer. This is a standard whole-exome library prep with tight insert size distribution around 225. The duplicate rate is showing between 25-30% from the 200X-targeted and 40-45% for the 400X targeted. I'm looking to report an accurate coverage estimate per library which appropriately considers ...
written 10 weeks ago by Dan D6.5k
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Is there any precedent for considering marked duplicates when calculating coverage in high-depth whole-exome sequencing?
... I'm working with some high-depth whole-exome sequencing data. It's paired-end. Some samples are targeted at 200X and others are 400X average read depth across the exome. The duplicate rate is very high after alignment. I suspect a good portion of these marked duplicates are not actual PCR duplicates ...
exome duplicates exome-seq coverage written 10 weeks ago by Dan D6.5k
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Answer: A: Removing Indices using Cutadapt
... OK, so let's look at a typical FASTQ read: @E00777:238:HABCDCCXY:1:1101:7770:2294 1:N:0:AGCGAAC ACAGTTGTCCAGTGGCAACAAGGACTCAAGAGATAGAAGACTGATATTATGGTATTTTGAACACCAGCTGAAACCCTTAGTGGCCGAATTTGTGCAGGTCT + -AAFFJJJJJF7AFJJAJJJJJAFJJJJ--FF-FF- ...
written 11 weeks ago by Dan D6.5k
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Comment: C: s. pombe alignment
... Can you please post the command lines you used? ...
written 3 months ago by Dan D6.5k
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Comment: C: IGV command line control
... Have you seen these? http://software.broadinstitute.org/software/igv/PortCommands http://software.broadinstitute.org/software/igv/batch ...
written 4 months ago by Dan D6.5k

Latest awards to Dan D

Appreciated 4 days ago, created a post with more than 5 votes. For A: what is in the fasta.fai
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Has anyone tried the new LFQC compression scheme for FASTQ?
Popular Question 3 months ago, created a question with more than 1,000 views. For Computational Biologist - Work with me at HudsonAlpha in Huntsville, USA
Popular Question 6 months ago, created a question with more than 1,000 views. For Computational Biologist - Work with me at HudsonAlpha in Huntsville, USA
Great Question 7 months ago, created a question with more than 5,000 views. For Anyone Have Suggestions For De Novo Assembly Of A Genome From Miseq 250 Pe Data?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Bwa or bowtie for mapping mulitple genomes
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Bwa or bowtie for mapping mulitple genomes
Popular Question 9 months ago, created a question with more than 1,000 views. For Computational Biologist - Work with me at HudsonAlpha in Huntsville, USA
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Bwa or bowtie for mapping mulitple genomes
Popular Question 9 months ago, created a question with more than 1,000 views. For Computational Biologist - Work with me at HudsonAlpha in Huntsville, USA
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Bwa or bowtie for mapping mulitple genomes
Scholar 11 months ago, created an answer that has been accepted. For A: Bwa or bowtie for mapping mulitple genomes
Appreciated 12 months ago, created a post with more than 5 votes. For A: what is in the fasta.fai
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For C: I want to re-open the old debate: python or perl ?
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Popular Question 14 months ago, created a question with more than 1,000 views. For Is There An Explanation For This Tophat "Yt" Descriptor Discrepancy In My Sam Output?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Bwa or bowtie for mapping mulitple genomes
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Scholar 19 months ago, created an answer that has been accepted. For A: Bwa or bowtie for mapping mulitple genomes
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Popular Question 2.1 years ago, created a question with more than 1,000 views. For Unable To Replicate Splice Junction In Tophat

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