Moderator: Brian Bushnell

gravatar for Brian Bushnell
Reputation:
16,180
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Trusted
Location:
Walnut Creek, USA
Website:
http://sourceforge.net...
Last seen:
3 months ago
Joined:
4 years, 7 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 18 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 19 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 19 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 19 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 20 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 20 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 20 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 20 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 20 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 20 months ago by Brian Bushnell16k

Latest awards to Brian Bushnell

Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Rename Duplicate ID's for Different Fasta Sequences on Windows 7
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: [samopen] SAM header is present: xxx sequences.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: exome sequencing, target capture
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to calculate genome side????
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: CUTADAPT in windows
Commentator 11 months ago, created a comment with at least 3 up-votes. For A: Phylogenetic trees from nucleotide sequence, nucleotide sequences of the entire
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Benchmark - Comparison of Different NGS Mappers
Scholar 11 months ago, created an answer that has been accepted. For A: why we still need PCR before NGS even when there are brige amplifications for si
Scholar 11 months ago, created an answer that has been accepted. For A: exome sequencing, target capture
Scholar 11 months ago, created an answer that has been accepted. For A: How to download human whole genome database?
Scholar 11 months ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: How to identify 16s sequences from binning data(contigs)?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Extending ends of sequences with the help of reads?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Duplicates on Illumina
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?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: How To Extract A Subset Of Reads In Fastq Using An Id List?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: How do I access genome coverage using SPADES?
Great Question 11 months ago, created a question with more than 5,000 views. For What does BAF mean?
Appreciated 11 months ago, created a post with more than 5 votes. For A: Why 50bp Illumina run produces 51bp long sequencs?
Appreciated 11 months ago, created a post with more than 5 votes. For A: Select sequences from fastq.gz file
Appreciated 11 months ago, created a post with more than 5 votes. For BBSketch - A Tool for Rapid Sequence Comparison
Appreciated 11 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?

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