User: Chronos

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Chronos590
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590
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Germany
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1 year, 7 months ago
Joined:
9 years, 5 months ago
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Posts by Chronos

<prev • 39 results • page 1 of 4 • next >
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Answer: A: AB1 to FASTQ
... If you wish to batch-convert hundreds of AB1 files, and you are comfortable with command line and compiling tools, then you can use TraceTuner, see [this thread][1] on seqanswers on how to add .fastq support to it. Another command-line solution would be to use `seqret` from the EMBOSS suite: `seqre ...
written 19 months ago by Chronos590
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Answer: A: An Existing Tool For Trimming Poly-A/T Tails Containing Single-Nucleotide Errors
... I've written the desired trimmer: https://bitbucket.org/qmentis/bioinformatics-scripts/src/566213e3da064e793857a7e06d9e77a43ec7ee28/sliding-window-polyA-trimmer.py?at=master On my PC, it processes 1m reads in a little under 20 seconds (10m reads in 3 minutes). Notes/bugs/features: it hasn't been ...
written 6.4 years ago by Chronos590
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Comment: C: An Existing Tool For Trimming Poly-A/T Tails Containing Single-Nucleotide Errors
... Right, trim_tail_left and trim_tail_right are the options I've used to get the second FastQC graph (the one after tail trimming). Assuming there's no existing solution, I've written a multi-threaded script to perform the desired sliding-window trimming. I'll test it tomorrow morning at work and wil ...
written 6.4 years ago by Chronos590
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Comment: C: Why Is Bwa Soft-Clipping Exactly Matching Reads?
... Might not be your case, but at least novoalign has an upper limit to the aligned read length. Last time I checked it was ~300 bp, and I think beyond that length it was soft-clipping the reads. I'm not entirely sure, though. ...
written 6.4 years ago by Chronos590
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Comment: C: Why Is Bwa Soft-Clipping Exactly Matching Reads?
... I wonder what the -M -NM options are for? I couldn't find them in the bwasw manual segment for my (possibly outdated) BWA 0.7.5... Are they a recent addition, or something undocumented? ...
written 6.4 years ago by Chronos590
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Comment: C: An Existing Tool For Trimming Poly-A/T Tails Containing Single-Nucleotide Errors
... AFAIK, trim_qual_window is only effective for quality trimming, not for poly-A/T trimming; low complexity filters are only used to filter away (remove) reads, not to trim them; custom_params is indeed an interesting option, but it is also listed in the filtering section, so I think it will discard ...
written 6.4 years ago by Chronos590
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An Existing Tool For Trimming Poly-A/T Tails Containing Single-Nucleotide Errors, Using A Sliding Window Approach?
... There exist multiple tools for trimming read poly-tails, but most of them seem to only look for the continuous stretch of the same nucleotide, and upon encountering a different nucleotide trimming stops. I'm using prinseq-lite.pl for trimming, and here are two graphs from FastQC - before and after t ...
fastq trimming written 6.4 years ago by Chronos590 • updated 5.7 years ago by Biostar ♦♦ 20
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Answer: A: Filter Polya/T And Other Repeats In Illumina Reads
... prinseq-lite, which is a fairly efficient command-line Perl script, supports two methods (dust and entropy, with adjustable thresholds) for removing low-complexity reads from your FASTQ files. It also has a separate option to trim poly-A/T tails, without discarding the entire read. ...
written 6.4 years ago by Chronos590
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Answer: A: What Kinds Of Software Can Be Used For Multi-Platform Microarray Normalization F
... Regarding normalization - see also Empirical comparison of cross-platform normalization methods for gene expression data, which provides the CONOR R-package with 9 methods for cross-platform normalization. ...
written 8.2 years ago by Chronos590
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Comment: C: How Does Ucsc Prepare Data For The Snp132 Table?
... Thanks, I've updated the question with the [overlooked] path to snpNcbiToUcsc.c ...
written 8.3 years ago by Chronos590

Latest awards to Chronos

Appreciated 5.1 years ago, created a post with more than 5 votes. For Why Total Exon Length Of 2/3Rds Of Ucsc Knowngenes Is Non-Divisible By 3?
Great Question 5.1 years ago, created a question with more than 5,000 views. For What Is Ad (Allelic Depth) In 1000Genomes Vcf?
Great Question 5.1 years ago, created a question with more than 5,000 views. For Phased And Unphased Genotypes In Vcf Files: Does The Order Of Alleles Matter?
Good Question 5.1 years ago, asked a question that was upvoted at least 5 times. For Why Total Exon Length Of 2/3Rds Of Ucsc Knowngenes Is Non-Divisible By 3?
Epic Question 5.1 years ago, created a question with more than 10,000 views. For What Is Ad (Allelic Depth) In 1000Genomes Vcf?
Epic Question 5.1 years ago, created a question with more than 10,000 views. For Phased And Unphased Genotypes In Vcf Files: Does The Order Of Alleles Matter?
Popular Question 5.1 years ago, created a question with more than 1,000 views. For 1000 Genomes: Where To Get Samples Description
Popular Question 5.1 years ago, created a question with more than 1,000 views. For How Does Ucsc Prepare Data For The Snp132 Table?
Voter 5.1 years ago, voted more than 100 times.
Appreciated 6.0 years ago, created a post with more than 5 votes. For What Is Ad (Allelic Depth) In 1000Genomes Vcf?
Appreciated 6.0 years ago, created a post with more than 5 votes. For Phased And Unphased Genotypes In Vcf Files: Does The Order Of Alleles Matter?
Good Question 6.0 years ago, asked a question that was upvoted at least 5 times. For What Is Ad (Allelic Depth) In 1000Genomes Vcf?
Good Question 6.0 years ago, asked a question that was upvoted at least 5 times. For Phased And Unphased Genotypes In Vcf Files: Does The Order Of Alleles Matter?
Popular Question 6.0 years ago, created a question with more than 1,000 views. For 1000 Genomes: Phased Or Not?
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Biosql Vs Own Db Schema For A Custom Snp + Annotations Data Storage
Popular Question 6.0 years ago, created a question with more than 1,000 views. For What Is Ad (Allelic Depth) In 1000Genomes Vcf?
Popular Question 6.0 years ago, created a question with more than 1,000 views. For 1000 Genomes: Where To Get Samples Description
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Phased And Unphased Genotypes In Vcf Files: Does The Order Of Alleles Matter?
Supporter 6.0 years ago, voted at least 25 times.
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Filter Polya/T And Other Repeats In Illumina Reads
Student 6.0 years ago, asked a question with at least 3 up-votes. For Biosql Vs Own Db Schema For A Custom Snp + Annotations Data Storage
Student 6.0 years ago, asked a question with at least 3 up-votes. For Why Total Exon Length Of 2/3Rds Of Ucsc Knowngenes Is Non-Divisible By 3?
Student 6.0 years ago, asked a question with at least 3 up-votes. For What Is Ad (Allelic Depth) In 1000Genomes Vcf?

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