Moderator: Brian Bushnell

gravatar for Brian Bushnell
Reputation:
10,140
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Trusted
Location:
Walnut Creek, USA
Website:
http://sourceforge.net...
Last seen:
54 minutes ago
Joined:
2 years, 4 months ago
Email:
b********@lbl.gov

I like to program in Java.

Posts by Brian Bushnell

<prev • 1,449 results • page 1 of 145 • next >
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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 8 hours 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 9 hours 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 9 hours 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 9 hours 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 9 hours ago by Brian Bushnell10k
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Comment: C: Faster way to get coverage per base
... The BBMap package has a tool "pileup.sh" which is quite fast, and produces per-base coverage from an unsorted sam or bam file. I'm not sure if this answers your question, though, as it's not clear to me whether you want bed as input or output, or need bed at all. ...
written 18 hours ago by Brian Bushnell10k
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Answer: A: Order of reads in FASTQ file
... Illumina reads are roughly in scan order. Nearby reads are likely to be nearby in the fastq. They are not ordered by quality. It depends on the instrument, but there are some universal truths (by "adjacent" I'm describing Illumina ordering): All reads in a lane are adjacent. All reads in a tile ...
written 1 day ago by Brian Bushnell10k
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Comment: C: Sequence filtration tool
... Hi Eslam, I recommend that you update your original post - right now it says: if you want to process a nucleotide sequences with a file containing list of exact names use the following command python sequence_filteration.py -in (input_file) -n -out (output_file) -filter (filter_file) -flt_mod ...
written 1 day ago by Brian Bushnell10k
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Comment: C: Minimum length in fastq quality trimmer with FASTX toolkit
... Both seqtk and BBDuk use the optimal Phred algorithm for quality-trimming, and both are very fast. I'd recommend either of them, though for paired reads I think BBDuk is more convenient. [Adapter-trimming][1] is probably at least as useful as quality-trimming, and BBDuk allows adapter-trimming sim ...
written 1 day ago by Brian Bushnell10k
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Comment: C: Why Freebayes Allele frequency(AF) is 0.5 or 1.0, instead of reporting actual al
... You can accept your own answer, by the way. ...
written 2 days ago by Brian Bushnell10k

Latest awards to Brian Bushnell

Commentator 1 day ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Commentator 2 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
Cylon 15 days ago, received 1,000 up votes.
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
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
Scholar 5 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Scholar 5 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
Scholar 5 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 6 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 6 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Scholar 6 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
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
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
Scholar 8 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates

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