Moderator: Dan D

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Dan D6.6k
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http://automationdan.com/
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Docendo discimus.

Posts by Dan D

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Answer: A: using bash variable in picard MarkDuplicates command
... The problem is not totally with your usage of variables. You're pointing Picard to the wrong location for the BAM (from the Picard output you pasted in the comment): Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: file:///home/cmccabe/NA12878.bam In your ...
written 3 months ago by Dan D6.6k
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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 5 months ago by Dan D6.6k
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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 6 months ago by Dan D6.6k
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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 6 months ago by Dan D6.6k
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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 6 months ago by Dan D6.6k
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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 6 months ago by Dan D6.6k
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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 6 months ago by Dan D6.6k
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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 6 months ago by Dan D6.6k • updated 11 days ago by marco_ul0
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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 6 months ago by Dan D6.6k
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Comment: C: s. pombe alignment
... Can you please post the command lines you used? ...
written 7 months ago by Dan D6.6k

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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?
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