Moderator: Brian Bushnell

gravatar for Brian Bushnell
Reputation:
10,250
Status:
Trusted
Location:
Walnut Creek, USA
Website:
http://sourceforge.net...
Last seen:
2 days, 21 hours ago
Joined:
2 years, 5 months ago
Email:
b********@lbl.gov

I like to program in Java.

Posts by Brian Bushnell

<prev • 1,454 results • page 1 of 146 • next >
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Comment: C: Which tool was used to generate this mapping file?
... I'd suggest you ignore those files, and use a standardized format like sam. Otherwise, the results of the experiment will not be reproducible. ...
written 3 days ago by Brian Bushnell10k
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Comment: C: Differences between trimming tools: cutadapt, bbduk and sickle
... "minavgquality=20" does not trim, it simply discards reads with an average quality below 20. I recommend trimming instead. And as Devon points out, 20 is too high for most purposes. I don't remember what trimming method is used by sickly or cutadapt, but BBDuk uses the phred algorithm, which leav ...
written 4 days ago by Brian Bushnell10k
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Comment: C: Target fragment size versus final insert size
... Oh, don't worry about that... reformat doesn't care in this case whether the reads are paired or not. They will be processed independently - so if you discard one read, its mate will not be discarded, but you're not discarding anything so it doesn't matter. ...
written 19 days ago by Brian Bushnell10k
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Comment: C: Minimum length in fastq quality trimmer with FASTX toolkit
... You can filter by gc content with BBDuk's mingc and maxgc flags, but that's a pretty crude way of filtering, since the peaks will overlap. It's usually better to filter the assembled contigs by gc since they are longer. As for plotting, I normally use Excel. ...
written 19 days ago by Brian Bushnell10k
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Comment: C: Faster way to get coverage per base
... Pileup will only allocate memory for chromosomes that actually have reads mapped to them, so yes. ...
written 26 days ago by Brian Bushnell10k
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Answer: A: Extracting fasta sequences with identical header
... You can use BBMap's FilterByName tool like this: filterbyname.sh in=x.fa out=y.fa names=z.fa include=t substring That will send everything to z.fa with headers matching those between x.fa and y.fa. The flag "substring" allows substring matches, which seems to be what you are seeking. ...
written 29 days ago by Brian Bushnell10k
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Comment: C: Double peaks on FASTQC
... Contamination from a different strain would not be obvious on a GC graph; they would completely overlap - contamination from a different strain is virtually impossible to detect. You can assemble, map the reads to the assembly, call variants, and view them in IGV to see if you have two strains in a ...
written 29 days ago by Brian Bushnell10k
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Answer: A: Number of reference sequence contigs in sam/bam header does not match the number
... The number of reference sequences comes from the aligner. Possibly, the aligner is ignoring sequences under a certain length, or all sequences that are entirely N. I suggest you skip masking/filtering, or record how many sequences you filtered, and try again. ...
written 29 days ago by Brian Bushnell10k
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Comment: C: Aligned the same reads to two similar genomes, want to filter for reads aligning
... As of now, BBMap is not capable of handling all bisulfite-altered reads. However, the package does contain a neat tool (bbsplit.sh) which will take an input fastq of reads and output multiple fastqs, based on which reference fasta they best match. Seal does the same thing, but uses kmer-matching r ...
written 29 days ago by Brian Bushnell10k
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Answer: A: Double peaks on FASTQC
... I suggest you simply go ahead with assembly, then BLAST the contigs. I think you probably have contamination by something, but it's much easier to detect and remove contamination once you have contig-length sequences, compared to reads. It could also be an organelle. ...
written 29 days ago by Brian Bushnell10k

Latest awards to Brian Bushnell

Good Answer 15 days ago, created an answer that was upvoted at least 5 times. For A: CUTADAPT in windows
Scholar 15 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Scholar 6 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Cylon 6 weeks ago, received 1,000 up votes.
Teacher 7 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 7 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Scholar 8 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
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
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
Scholar 9 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
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 9 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
Scholar 10 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Scholar 11 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 11 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 11 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 11 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates

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