Moderator: Brian Bushnell

gravatar for Brian Bushnell
Reputation:
17,250
Status:
Trusted
Location:
Walnut Creek, USA
Website:
http://sourceforge.net...
Last seen:
4 months, 2 weeks ago
Joined:
5 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
... Optical duplicates can be detected by adding the "optical" flag to Clumpify if the Illumina reads still have original headers, though the exact settings depend on the platform. PCR duplicates cannot be detected and differentiated from coincidental duplicates with high confidence in RNA-seq librarie ...
written 4 months ago by Brian Bushnell17k
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Answer: A: Current challenges in SARS-CoV-2 analysis?
... There are many challenges here. @[gb][1], it was not wrong of you to mention regulations; those are one of the biggest challenges with Covid-19 bioinformatics. Due to privacy regulations, people change their experimental design and processing pipelines, and restrict data-sharing, to reduce the ris ...
written 6 months ago by Brian Bushnell17k
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Comment: C: BBSketch - A Tool for Rapid Sequence Comparison
... Yes, catting would work; in addition to catting the files, you can also stream them to stdin: cat *.fasta | sketch.sh in=stdin.fa onesketch out=xyz.sketch That said, I'm not sure why you would want to make one sketch for thousands of fasta files. If you want one sketch per input file, with al ...
written 9 months ago by Brian Bushnell17k • updated 9 months ago by genomax91k
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Comment: C: viral genome assembly
... Tadpole seems to do a better job of assembling viruses than Spades. I won't guarantee that, but it seems to be generally true. Viruses and hosts can share sequence. If you remove all sequences shared between the virus and host, it's likely that you will incur holes in your assembly, if you are tr ...
written 10 months ago by Brian Bushnell17k
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Answer: A: rRNA decontamination of RNA-Seq reads (tool choice, introns etc)
... BBDuk is a filter. At JGI we use it to remove reads with 31-mers corresponding to common ribosomal 31-mers, because some downstream tools like Trinity fail when there is an overload of rRNA reads. Running BBDuk with common ribosomal kmers is good practice, but not ideal; the sensitivity and specif ...
written 10 months ago by Brian Bushnell17k
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Comment: C: BBTools/BBMap/BBSuite's sketch.sh and sendsketch.sh are inconsistent
... I just revised all of the fetch scripts in 38.61b which I released today. You should be able to do this: Run fetchTaxonomy.sh Then modify fetchNt.sh to change the line TAXPATH="auto" to point to wherever you downloaded the taxonomy data. Then run fetchNt.sh. That will give you nt which is not as ...
written 14 months ago by Brian Bushnell17k
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Comment: C: BBTools/BBMap/BBSuite's sketch.sh and sendsketch.sh are inconsistent
... OK, all servers are back up again! RefSeq is the default server. You can specify: refseq, protein, nt, or ribo (aka silva). It will only connect to one server each time you run it. ...
written 15 months ago by Brian Bushnell17k
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Answer: C: BBTools/BBMap/BBSuite's sketch.sh and sendsketch.sh are inconsistent
... The important thing here is: Query: scaffolds.drop_bacteria.fasta DB: RefSeq **SketchLen: 52788 Seqs: 738 Bases: 82339741** In every case it used all 738 sequences and 82Mbp, and made one sketch, though the sketch size was different in the two cases since the RefSeq server uses larger-tha ...
written 15 months ago by Brian Bushnell17k • updated 15 months ago by genomax91k
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Comment: C: BBSketch - A Tool for Rapid Sequence Comparison
... BBSketch servers are hosted on NERSC, which is down for ~5 days starting at 8am PST this morning for electrical work. Unfortunately, that means that they are also down. In fact, everything at JGI is down until Monday or Tuesday night. ...
written 15 months ago by Brian Bushnell17k
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Comment: C: BBSketch - A Tool for Rapid Sequence Comparison
... If it has super-low identity to anything in RefSeq, Sketch will not be able to identify it correctly. In this case the nucleotide hits are totally random; they only shared 3 sketch kmers, with estimated ANI under 76%, and Sketch is *not* accurate at under 76% ANI. The protein results are much more ...
written 15 months ago by Brian Bushnell17k

Latest awards to Brian Bushnell

Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to calculate genome side????
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Denovo assembly SPAdes ERROR K-mer Counting: too many k-mers to fit into availab
Appreciated 6 months ago, created a post with more than 5 votes. For A: Filter Bacterial sequences from Metagenomics
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to calculate genome side????
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: [samopen] SAM header is present: xxx sequences.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: exome sequencing, target capture
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to calculate genome side????
Scholar 9 months ago, created an answer that has been accepted. For A: How to download human whole genome database?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to calculate genome side????
Scholar 10 months ago, created an answer that has been accepted. For A: How to download human whole genome database?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to calculate genome side????
Scholar 10 months ago, created an answer that has been accepted. For A: How to download human whole genome database?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: exome sequencing, target capture
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to calculate genome side????
Scholar 14 months ago, created an answer that has been accepted. For A: when the local alignment tends to work as global alignment?
Scholar 14 months ago, created an answer that has been accepted. For A: bwa mem multiple alignments doesn't work
Scholar 14 months ago, created an answer that has been accepted. For A: bwa mapping after fastx-trimmer
Scholar 14 months ago, created an answer that has been accepted. For A: How to search miseq data for large mutations
Scholar 14 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 14 months ago, created an answer that has been accepted. For A: exome sequencing, target capture
Scholar 14 months ago, created an answer that has been accepted. For A: How to download human whole genome database?
Pundit 14 months ago, created a comment with more than 10 votes. For C: Trimming adapter sequences - is it necessary?
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: How do I access genome coverage using SPADES?
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Why 50bp Illumina run produces 51bp long sequencs?

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