Moderator: Brian Bushnell

gravatar for Brian Bushnell
Reputation:
14,480
Status:
Trusted
Location:
Walnut Creek, USA
Website:
http://sourceforge.net...
Last seen:
1 week, 4 days ago
Joined:
3 years ago
Email:
b********@lbl.gov

I like to program in Java.

Posts by Brian Bushnell

<prev • 1,919 results • page 1 of 192 • next >
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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 days ago by Brian Bushnell14k
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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 23 days ago by Brian Bushnell14k
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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 23 days ago by Brian Bushnell14k
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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 4 weeks ago by Brian Bushnell14k
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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 5 weeks ago by Brian Bushnell14k
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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 5 weeks ago by Brian Bushnell14k
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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 5 weeks ago by Brian Bushnell14k
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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 5 weeks ago by Brian Bushnell14k
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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 5 weeks ago by Brian Bushnell14k
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Comment: C: how to make a .bam file from fastQ for RNA-seq ion torrent with BBmap
... For human RNA-seq you should add the flag "maxindel=400k". You don't need to change anything else. ...
written 6 weeks ago by Brian Bushnell14k

Latest awards to Brian Bushnell

Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Why 50bp Illumina run produces 51bp long sequencs?
Good Answer 25 days ago, created an answer that was upvoted at least 5 times. For A: Why 50bp Illumina run produces 51bp long sequencs?
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: SPAdes assembler k-mer > default 127 possible?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Use jellyfish with paired end sequencing data
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Benchmark - Comparison of Different NGS Mappers
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: SPAdes assembler k-mer > default 127 possible?
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Benchmark - Comparison of Different NGS Mappers
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Scholar 9 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Scholar 10 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
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
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
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Duplicates on Illumina
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: Benchmark - Comparison of Different NGS Mappers
Popular Question 11 weeks ago, created a question with more than 1,000 views. For BBSketch - A Tool for Rapid Sequence Comparison
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Duplicates on Illumina
Scholar 12 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training

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