Moderator: Brian Bushnell

gravatar for Brian Bushnell
Brian Bushnell9.8k
Reputation:
9,810
Status:
Trusted
Location:
Walnut Creek, USA
Website:
http://sourceforge.net...
Last seen:
3 hours ago
Joined:
2 years, 3 months ago
Email:
b********@lbl.gov

I like to program in Java.

Posts by Brian Bushnell

<prev • 1,370 results • page 1 of 137 • next >
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Comment: C: BWA mem output inconsistent on same but re-ordered FASTQ input
... Right... again, that's not exactly unexpected, so why are you surprised? 10000 is too small a number of reads to use for statistics, particularly if you did not sample them randomly from the dataset (which you did not state). Also, please post your responses as a response, rather than an answer, ...
written 1 day ago by Brian Bushnell9.8k
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Comment: C: Bacterial sequence reads supporting two nucleotides at same location
... Sorry, but no, I have zero experience in writing or using SV callers. ...
written 1 day ago by Brian Bushnell9.8k
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Comment: C: Trim Reads From BAM files
... So, what exactly are you trying to do? And why? ...
written 1 day ago by Brian Bushnell9.8k
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Comment: C: Denovo assembly SPAdes ERROR K-mer Counting: too many k-mers to fit into availab
... Hi Ambi, I'm happy BBNorm was helpful in this case! To close this thread as resolved, if you feel that is has in fact been resolved, please accept the answer. Thanks, Brian ...
written 1 day ago by Brian Bushnell9.8k
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Comment: C: Choosing de novo genome assembly
... Oh, nice! That's much less annoying than h5. ...
written 1 day ago by Brian Bushnell9.8k
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Comment: C: What are the methods and recources of filtering contigs after de novo genome ass
... There is no recipe for decontamination. You need to use your judgement. ...
written 1 day ago by Brian Bushnell9.8k
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Comment: C: Bacterial sequence reads supporting two nucleotides at same location
... It's certainly possible that there are multiple genotypes in your sample. But also, I see this a lot with supposedly pure samples, as a result of structural variations. There are a few SNPs that differ from the reference, with extremely high confidence (like, 98% of the reads indicating it)... tho ...
written 1 day ago by Brian Bushnell9.8k
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Comment: C: Change paired end library from FR to RF
... Glad to hear it! If you think this answer resolved the question, please "accept" it so that other people know it is resolved. ...
written 1 day ago by Brian Bushnell9.8k
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Comment: C: Choosing de novo genome assembly
... Great post! But, can I ask you to clarify this line: "I'm just warning you that PacBio tools are actually being deeply changed (they want to leave the bas/bax//cmp.h5 files extensions to propose classic fasta/sam/bam files." It's not quite clear what it means - whether PacBio is migrating *to* or ...
written 1 day ago by Brian Bushnell9.8k
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Comment: C: What is the fastest way to add 'Ns' to variable length sequences in a .fasta suc
... You might be using the wrong for the job. Good tools don't have strange and arbitrary requirements to mutate your data before they work. Also, it makes absolutely no sense for read 2 to be shorter than read 1 after adapter-trimming. They should be the same length, since the adapter sequence will ...
written 1 day ago by Brian Bushnell9.8k

Latest awards to Brian Bushnell

Scholar 1 day ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Scholar 7 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Scholar 7 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Commentator 11 days ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Scholar 12 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Scholar 12 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Scholar 18 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Scholar 20 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Scholar 25 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Scholar 28 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 4 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 4 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 4 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 4 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 5 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 5 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 5 weeks ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming

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