Moderator: Dan D
Dan D ♦ 6.8k
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Docendo discimus.
Posts by Dan D
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... 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 11 months ago by
Dan D ♦ 6.8k
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... 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 ...
written 13 months ago by
Dan D ♦ 6.8k
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48
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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 14 months ago by
Dan D ♦ 6.8k
0
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376
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... 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 14 months ago by
Dan D ♦ 6.8k
0
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1
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724
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... 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 14 months ago by
Dan D ♦ 6.8k
0
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1
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724
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1
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... Oh, right, I didn't address that in my reply. I will give it a try right now. ...
written 14 months ago by
Dan D ♦ 6.8k
0
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724
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... @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 14 months ago by
Dan D ♦ 6.8k
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5 follow
1
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... 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 ...
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... 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 14 months ago by
Dan D ♦ 6.8k
0
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1
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474
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1
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Comment:
C: s. pombe alignment
... Can you please post the command lines you used? ...
written 15 months ago by
Dan D ♦ 6.8k
Latest awards to Dan D
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11 weeks ago,
created a post with more than 5 votes.
For A: What is the best programming language for NGS data analysis pipeline development
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8 months ago,
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For Should quality scores be considered when discriminating between optical and library duplicates?
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For C: I want to re-open the old debate: python or perl ?
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For Has anyone tried the new LFQC compression scheme for FASTQ?
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For Anyone Have Suggestions For De Novo Assembly Of A Genome From Miseq 250 Pe Data?
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For A: Bwa or bowtie for mapping mulitple genomes
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For C: I want to re-open the old debate: python or perl ?
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For A: Bwa or bowtie for mapping mulitple genomes
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