Moderator: Chris Miller

gravatar for Chris Miller
Chris Miller17k
Reputation:
17,460
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Trusted
Location:
Washington University in St. Louis, MO
Website:
http://www.chrisamille...
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Google Scholar Page
Last seen:
1 day, 10 hours ago
Joined:
7 years 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 • 926 results • page 2 of 93 • next >
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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 3 months 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 3 months ago by Chris Miller17k
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Comment: C: How to do INDEL alignment
... edited to fix broken URL ...
written 3 months 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 3 months 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 3 months 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 3 months 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 3 months ago by Chris Miller17k
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Comment: C: What is the coverage when allele frequency is < 1?
... One additional comment on your plan. Somatic variants will occur on both copies of the genome, so your plan to mutate one fastq and not the other, then generate reads, is flawed. (your mutations will always be seen in phase, where phasing is resolvable) ...
written 3 months ago by Chris Miller17k
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Comment: C: What is the coverage when allele frequency is < 1?
... FWIW, when talking about ploidy, we are talking about copy number (amplification or deletions) ...
written 3 months ago by Chris Miller17k
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Comment: C: samtools sort generates over millions of files
... you should start by adding the command that you used ...
written 3 months ago by Chris Miller17k

Latest awards to Chris Miller

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Popular Question 21 days ago, created a question with more than 1,000 views. For Importing A Large Number Of References From Text
Scholar 5 weeks ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Appreciated 5 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Appreciated 8 weeks ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated 3 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Extract Base Based On Position From Bam File
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Scholar 3 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Hardware Suitable For Generic Nextgen Sequencing Processing?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Music Smashing The Stack
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Aligning Reads To Specific Chromosome Using Bwa
Appreciated 6 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Appreciated 6 months ago, created a post with more than 5 votes. For C: Should Biostar Be Switched Over To The Stackexchange Network?
Great Question 7 months ago, created a question with more than 5,000 views. For Bioinformatics "Cheat Sheet"
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
Appreciated 8 months ago, created a post with more than 5 votes. For A: Difference Between Somatic And Germline Variant Calling?
Scholar 9 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome
Scholar 9 months ago, created an answer that has been accepted. For A: Spliting a dataframe based in a chromosome

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