Moderator: Brian Bushnell

gravatar for Brian Bushnell
Reputation:
15,540
Status:
Trusted
Location:
Walnut Creek, USA
Website:
http://sourceforge.net...
Last seen:
3 months, 1 week ago
Joined:
3 years, 11 months ago
Email:
b********@lbl.gov

I like to program in Java.

Posts by Brian Bushnell

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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 10 months ago by Brian Bushnell16k
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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 11 months ago by Brian Bushnell16k
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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 11 months ago by Brian Bushnell16k
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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 11 months ago by Brian Bushnell16k
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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 12 months ago by Brian Bushnell16k
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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 12 months ago by Brian Bushnell16k
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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 12 months ago by Brian Bushnell16k
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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 12 months ago by Brian Bushnell16k
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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 12 months ago by Brian Bushnell16k
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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 12 months ago by Brian Bushnell16k

Latest awards to Brian Bushnell

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: [samopen] SAM header is present: xxx sequences.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: exome sequencing, target capture
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to calculate genome side????
Teacher 8 months 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 8 months ago, created a question with more than 1,000 views. For Introducing CrossBlock, a BBTool for removing cross-contamination
Popular Question 8 months ago, created a question with more than 1,000 views. For BBSketch - A Tool for Rapid Sequence Comparison
Appreciated 8 months ago, created a post with more than 5 votes. For A: Why 50bp Illumina run produces 51bp long sequencs?
Appreciated 8 months ago, created a post with more than 5 votes. For A: How To Extract A Subset Of Reads In Fastq Using An Id List?
Appreciated 8 months ago, created a post with more than 5 votes. For NovaSeq quality analysis
Appreciated 8 months ago, created a post with more than 5 votes. For C: merge large amount of fastq files into a single one
Teacher 8 months 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 8 months ago, created a question with more than 1,000 views. For BBSketch - A Tool for Rapid Sequence Comparison
Popular Question 10 months ago, created a question with more than 1,000 views. For BBSketch - A Tool for Rapid Sequence Comparison
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Duplicates on Illumina
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Why 50bp Illumina run produces 51bp long sequencs?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Why 50bp Illumina run produces 51bp long sequencs?
Popular Question 10 months ago, created a question with more than 1,000 views. For BBSketch - A Tool for Rapid Sequence Comparison
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Why 50bp Illumina run produces 51bp long sequencs?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Why 50bp Illumina run produces 51bp long sequencs?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Why 50bp Illumina run produces 51bp long sequencs?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: SPAdes assembler k-mer > default 127 possible?

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