Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller17k
Reputation:
17,180
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Trusted
Location:
Washington University in St. Louis, MO
Website:
http://www.chrisamille...
Scholar ID:
Google Scholar Page
Last seen:
3 days, 2 hours ago
Joined:
6 years, 10 months ago
Email:
c***********@gmail.com

I work in the Genome Institute at Washington University in St. Louis, where I lead a group that develops and applies computational tools to give us insight into the origins and progression of cancer.

Posts by Chris Miller

<prev • 919 results • page 1 of 92 • next >
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Answer: A: Correcting for tumor purity in tumor evolution analysis
... Most experienced cancer genomic folks will agree that pathology estimates of tumor content are often inaccurate. If the genomic sequencing tells you that the VAFs max out at 20, then your sample is likely 40% tumor (and 60% non tumor - normal contamination). That said, there may be cases where you ...
written 9 days ago by Chris Miller17k
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Comment: C: fastq.gz Error: Not in gzip format
... "file" should be a valid command on just about any *nix system. Did it output an error or what? ...
written 28 days ago by Chris Miller17k
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Comment: C: fastq.gz Error: Not in gzip format
... What OS are you using? ...
written 28 days ago by Chris Miller17k
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Answer: A: fastq.gz Error: Not in gzip format
... Well, start by making sure that they're gzipped files and not just errantly named: $ file tmp.gz tmp.gz: gzip compressed data,was "tmp", from Unix, last modified: Tue Dec 13 13:12:02 2016, max compression Also try opening it without unzipping less file.gz If the output comes back as ...
written 28 days ago by Chris Miller17k
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Answer: A: BAM to FASTQ
... Samtools is not the right tool for this job. Try bedtools bamtofastq (after name-sorting your bam): https://bedtools.readthedocs.io/en/latest/content/tools/bamtofastq.html ...
written 4 weeks ago by Chris Miller17k
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Comment: C: How to do INDEL alignment
... edited to fix broken URL ...
written 4 weeks ago by Chris Miller17k
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Comment: C: BAM to Fastq using picard and others from a desired regions
... Makes sense - good detective work! ...
written 5 weeks ago by Chris Miller17k
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Comment: C: BAM to Fastq using picard and others from a desired regions
... Sounds like you are still skipping reads that have only one of the pairs, then. You can either put those back in manually (by finding read names that only appear once, then converting to a non-paired fastq file to go along with your paired data), or try to figure out why they're still missing. Are t ...
written 5 weeks ago by Chris Miller17k
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Comment: C: How to cite the "BED 12" format ?
... Generally speaking, you don't need citations for a file format... ...
written 5 weeks ago by Chris Miller17k
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Answer: A: BAM to Fastq using picard and others from a desired regions
... If I understand your question correctly, it boils down to "How can I extract all reads within a region and their paired reads (which may be mapped elsewhere)?" See these two previous answers: - https://www.biostars.org/p/105714/ - https://www.biostars.org/p/68358/#68362 Once you have that bam (an ...
written 5 weeks ago by Chris Miller17k

Latest awards to Chris Miller

Appreciated 29 days ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 4 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Extract Base Based On Position From Bam File
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: Hardware Suitable For Generic Nextgen Sequencing Processing?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Appreciated 4 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated 4 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Great Question 5 months ago, created a question with more than 5,000 views. For Bioinformatics "Cheat Sheet"
Scholar 5 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Appreciated 6 months ago, created a post with more than 5 votes. For A: Difference Between Somatic And Germline Variant Calling?
Scholar 7 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 7 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: All Possible Substitutions In The Human Reference Genome
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 8 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome

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