Moderator: Brian Bushnell
Brian Bushnell ♦ 17k
- Reputation:
- 17,250
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- 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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... 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 Bushnell ♦ 17k
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... 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 Bushnell ♦ 17k
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... 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 Bushnell ♦ 17k
• updated
9 months ago by
genomax ♦ 91k
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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 Bushnell ♦ 17k
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... 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 Bushnell ♦ 17k
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... 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 Bushnell ♦ 17k
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... 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 Bushnell ♦ 17k
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... 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 Bushnell ♦ 17k
• updated
15 months ago by
genomax ♦ 91k
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... 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 Bushnell ♦ 17k
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... 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 Bushnell ♦ 17k
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
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9 months ago,
created an answer with at least 3 up-votes.
For A: How to calculate genome side????
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9 months ago,
created an answer that has been accepted.
For A: How to download human whole genome database?
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9 months ago,
created a question with more than 5,000 views.
For Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
Teacher
10 months ago,
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For A: How to calculate genome side????
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10 months ago,
created an answer that has been accepted.
For A: How to download human whole genome database?
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For A: How to calculate genome side????
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10 months ago,
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For A: How to download human whole genome database?
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14 months ago,
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For A: exome sequencing, target capture
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14 months ago,
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For A: How to calculate genome side????
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For A: when the local alignment tends to work as global alignment?
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For A: bwa mem multiple alignments doesn't work
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For A: bwa mapping after fastx-trimmer
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For A: How to search miseq data for large mutations
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For A: why we still need PCR before NGS even when there are brige amplifications for si
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For A: exome sequencing, target capture
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14 months ago,
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For A: How to download human whole genome database?
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14 months ago,
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For C: Trimming adapter sequences - is it necessary?
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14 months ago,
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For A: How do I access genome coverage using SPADES?
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For A: Why 50bp Illumina run produces 51bp long sequencs?
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