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Moderator: Brian Bushnell

gravatar for Brian Bushnell
Reputation:
14,940
Status:
Trusted
Location:
Walnut Creek, USA
Website:
http://sourceforge.net...
Last seen:
1 month, 3 weeks ago
Joined:
3 years, 5 months ago
Email:
b********@lbl.gov

I like to program in Java.

Posts by Brian Bushnell

<prev • 1,920 results • page 1 of 192 • next >
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
... I develop and test BBTools under Oracle JDK. For most programs, there's no significant difference between Oracle and OpenJDK. However, in some programs that use nearly all available memory, the conditions for memory crashes are different, as the two JVMs manage memory differently. For example, I ...
written 4 months ago by Brian Bushnell ♦ 15k
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Comment: C: Introducing CrossBlock, a BBTool for removing cross-contamination
... Hi Andrew, Yes, a log file would be essential here so I can see what phase it's stopping at. Additionally, the entire command line, and contents of readnamefile and refnamefile (if you used those), would be helpful, as would the BBMap version. To clarify, are these transcriptomes of three differe ...
written 5 months ago by Brian Bushnell ♦ 15k
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
... Oh, hmm, that's odd. I guess I did not read the question carefully enough. Let me edit that post... ...
written 5 months ago by Brian Bushnell ♦ 15k
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
... > It's smaller because the sorted reads compress more efficiently than > unsorted reads, since reads sharing sequence are adjacent in the file. > The number of reads is the same. If you decompress the files they > will be the same size. Edit - for some reason I overlooked the fact that ...
written 5 months ago by Brian Bushnell ♦ 15k
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Comment: C: Calling SNPs with low coverage
... Oh, that version is too old. CallVariants was not added until v36.55 (but I recommend the latest, 37.61). ...
written 5 months ago by Brian Bushnell ♦ 15k
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Answer: A: How to make variant calling run faster?
... You can make variant-calling much faster by using BBMap's callvariants.sh tool (which is fully multithreaded) on a raw, unsorted sam file, so you don't have to waste time sorting, indexing and compressing/decompressing bam. It works on bam files too, though, so if you want to use a bam as input I s ...
written 6 months ago by Brian Bushnell ♦ 15k
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Comment: C: how to make a .bam file from fastQ for RNA-seq ion torrent with BBmap
... I can't really help you if you don't answer my questions. It sounds likely that you have contamination. I suggest you try BLASTing some reads to see what they hit. ...
written 6 months ago by Brian Bushnell ♦ 15k
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Answer: A: Unsynchronized simultaneous reads on a single .bam file
... Simultaneous reads don't cause problems; concurrency problems only occur when there is a mix of reads and writes. 100% reads or 100% writes are fine (100% writes is fine because the data is never read so the final state cannot be observed). Some filesystems may perform better or worse with lots of ...
written 6 months ago by Brian Bushnell ♦ 15k
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Comment: C: NGS statistics - Mean coverage and % of bases >20x (or probability to miss one o
... You might be able to get a useful value by also incorporating the standard deviation, some other measure of variance, and/or additional variables, but not with a single universal closed-form equation using the coverage alone. Different library preparation, amplification, and sequencing platforms gr ...
written 6 months ago by Brian Bushnell ♦ 15k
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Comment: C: how to make a .bam file from fastQ for RNA-seq ion torrent with BBmap
... BBMap should not need any special parameters for Ion Torrent data. Perhaps you could post your command and the stderr output? ...
written 6 months ago by Brian Bushnell ♦ 15k

Latest awards to Brian Bushnell

Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Popular Question 10 weeks ago, created a question with more than 1,000 views. For BBSketch - A Tool for Rapid Sequence Comparison
Popular Question 4 months ago, created a question with more than 1,000 views. For BBSketch - A Tool for Rapid Sequence Comparison
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Duplicates on Illumina
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Why 50bp Illumina run produces 51bp long sequencs?
Prophet 4 months ago, created a post with more than 20 followers. For Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Why 50bp Illumina run produces 51bp long sequencs?
Popular Question 4 months ago, created a question with more than 1,000 views. For BBSketch - A Tool for Rapid Sequence Comparison
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Why 50bp Illumina run produces 51bp long sequencs?
Appreciated 5 months ago, created a post with more than 5 votes. For Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Why 50bp Illumina run produces 51bp long sequencs?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Why 50bp Illumina run produces 51bp long sequencs?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: SPAdes assembler k-mer > default 127 possible?
Scholar 6 months ago, created an answer that has been accepted. For A: Use jellyfish with paired end sequencing data
Appreciated 6 months ago, created a post with more than 5 votes. For Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
Appreciated 6 months ago, created a post with more than 5 votes. For Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Benchmark - Comparison of Different NGS Mappers
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: SPAdes assembler k-mer > default 127 possible?
Appreciated 6 months ago, created a post with more than 5 votes. For Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Benchmark - Comparison of Different NGS Mappers
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Appreciated 6 months ago, created a post with more than 5 votes. For Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
Scholar 7 months ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Scholar 7 months ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
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