User: Richard

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Richard500
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500
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Canada
Last seen:
8 months ago
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5 years, 7 months ago
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r****************@gmail.com

Posts by Richard

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Comment: C: proximal duplicate parameters - HiSeq X
... ![][1] I used some test HiSeq X data and tried a number of pixel distances. It does seem that the distance of about 2500 is about the saturation point for identifying duplicates as optical [1]: http://www.bcgsc.ca/downloads/rcorbett/proximalTest.png "proximal distance" ...
written 8 months ago by Richard500
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proximal duplicate parameters - HiSeq X
... Hi all, We are doing some QC on our HiSeqX genome data. Here we see an increased rate of duplicates for the same libraries sequenced on other platforms. This is a known phenomenon as mentioned in this post on the GATK website: http://gatkforums.broadinstitute.org/gatk/discussion/6747/how-to-ma ...
duplicates proximal written 8 months ago by Richard500 • updated 8 months ago by genomax34k
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does bwa mem use base qualities?
... Hi all, I've been looking around on the internet for confirmation that BWA mem doesn't use base qualities.    Can anyone confirm that BWA mem does not use the base qualities: To decide where an alignment should be placed To assign a mapping quality I see in the docs that it does/can use the b ...
bwa written 21 months ago by Richard500
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auto trimming of adapter and 6 base normalizing sequence from miRNA reads
... Hi all, Apologies if my terminology isn't correct on this one... I'm used to looking at microRNA reads from which I need to trim some amount of adapter off the ends.   I have a simple script to take care of this that works relatively well.    However, I'm starting to look at microRNA data from a d ...
adapters trimming microrna written 22 months ago by Richard500 • updated 1 day ago by Biostar ♦♦ 20
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Answer: C: Affy 500K positions in hg38
... If anyone needs to know how I ended up figuring this out.  I downloaded the annotation CSV files from here (these files have hg19 coords), and joined the rs IDs against a dbSNP VCF: http://www.affymetrix.com/catalog/131459/AFFY/Mapping+500K+Array+Set#1_3   ...
written 22 months ago by Richard500
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Affy 500K positions in hg38
... Hi all, Does anyone know where one can find a list of the Affy 500K SNP positions in hg38 coordinates? ...
hg38 affymetrix written 22 months ago by Richard500 • updated 22 months ago by Sean Davis23k
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Comment: C: variant calling on amplicon data
... For now, it is a limitation of our pipeline - that all bams are duplicate marked when they come through. ...
written 2.1 years ago by Richard500
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variant calling on amplicon data
... Hi all, Does anyone have a recommended approach for variant calling (SNVs and indels) on human amplicon illumina reads?  My bams are aligned with BWA and have had the chastity failed and duplicate reads marked. If possible, I'd like to be able to apply a variant caller that can be instructed to ig ...
amplicon variant written 2.1 years ago by Richard500 • updated 2.1 years ago by Zaag610
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Answer: A: Identify somatic mutations in cancer exome without a matched pair.
... I have been working on something similar (using genomes). Here is what I've learned so far: -This is unfortunately more difficult than I originally hoped.   For example, general knowledge is that variants found in COSMIC will be somatic in other samples, when in practice I've flagged many variants ...
written 2.1 years ago by Richard500
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fastq compression tools of choice
... Hi all, I'll be trying out a few compression tools for fastq files.   So far on my list I have the following: dsrc lrzip gzip bgzf Anyone have any good/poor experience with any of the above, or other options? I'll be trying them all plotting compression ratio vs. (comp, decomp) cpu time, b ...
fatq compression written 2.1 years ago by Richard500

Latest awards to Richard

Great Question 10 months ago, created a question with more than 5,000 views. For Tophat-Fusion-Post Error
Popular Question 10 months ago, created a question with more than 1,000 views. For Fasta Output Python Parsing
Popular Question 11 months ago, created a question with more than 1,000 views. For Fasta Output Python Parsing
Popular Question 11 months ago, created a question with more than 1,000 views. For Mate Pair Alignment Summary
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Popular Question 17 months ago, created a question with more than 1,000 views. For Mate Pair Alignment Summary
Popular Question 17 months ago, created a question with more than 1,000 views. For Biopython Examples For Writing Genbank Files?
Popular Question 17 months ago, created a question with more than 1,000 views. For Blast Indel Calibration
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Student 18 months ago, asked a question with at least 3 up-votes. For sam/bam file handling -> new tools?
Popular Question 21 months ago, created a question with more than 1,000 views. For Need Recommendations For Aligning Longer (2X250Bp) Reads
Great Question 2.1 years ago, created a question with more than 5,000 views. For Standalone Blast 2 Short Sequences
Supporter 2.1 years ago, voted at least 25 times.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Need Recommendations For Aligning Longer (2X250Bp) Reads
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Need Recommendations For Aligning Longer (2X250Bp) Reads
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Student 5.0 years ago, asked a question with at least 3 up-votes. For Need Recommendations For Aligning Longer (2X250Bp) Reads
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Blast Indel Calibration
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Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Coverage In Bam Alignment

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