Moderator: Damian Kao

gravatar for Damian Kao
Damian Kao15k
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http://blog.nextgeneti...
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Bioinformatician at Janelia Research Campus.

Posts by Damian Kao

<prev • 884 results • page 1 of 89 • next >
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Best practices for variant calling on multiple sequencing runs of the same sample
... Given a single DNA sample extracted from swab and these two cases: 1. Prepared a single library and sequenced it 3 times separately 2. Prepared 3 different libraries from the same DNA sample and sequenced each library Both cases result in 3 sets of fastqs. Case 1 representing technical replica ...
variant calling vcf snps written 5 days ago by Damian Kao15k • updated 5 days ago by swbarnes24.1k
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Answer: A: 20-mer DNA sequence list - assess similarity
... Starcode is for UMI clustering, but it should also work for your purposes: https://github.com/gui11aume/starcode ...
written 19 days ago by Damian Kao15k
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Comment: C: Pseudogenes in bacteria genome
... Is this a genome that you have assembled yourself? Could these be assembly artifacts? ...
written 7 weeks ago by Damian Kao15k
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Answer: A: Is there consensus on what constitutes a good BUSCO score?
... I think relative BUSCO comparisons are more informative than absolute BUSCO scores. For example, using BUSCO to compare various assemblies of the same data. If you have the computation resources, you can also perform a saturation curve of input reads to BUSCO scores. For example, take random subset ...
written 7 weeks ago by Damian Kao15k
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Comment: C: covert SAM to full length fasta
... We don't know what exactly you are looking for. I can think of: 1) You want to get a fasta of all loci on the genome that has at least one read mapping? 2) You want to get a fasta of "consensus" reads. There is no consensus, since there might be SNPs/variants. You could potentially have two or mor ...
written 8 weeks ago by Damian Kao15k
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Comment: C: Is there a easy to use GATK pipeline for SNP calling?
... GATK best practices suggest creating a genome VCF (g.vcf) for each individual, combining the g.vcfs and then doing a joint-calling. This is step 4,5,6 in my comment. A genome VCF is different from a normal VCF in that it will also output information on positions that are not different from the ref ...
written 8 weeks ago by Damian Kao15k
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Comment: C: Is there a easy to use GATK pipeline for SNP calling?
... Yes, I usually just use picardtools' MarkDuplicates. Duplicate/recombinant regions are tricky to deal with. It might be better to do some kind of de novo assembly of those regions specifically if that's what you want to study. ...
written 8 weeks ago by Damian Kao15k
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Answer: A: sed regex code help wanted
... If all your lines have ID_genus_species only (3 items), then you can probably just use cut: cut -f 2,3 -d '_' input.file ...
written 8 weeks ago by Damian Kao15k
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Answer: A: What is wrong with NCBI's gff file?
... Gene, mRNA and Exon starting with the same coordinate is normal. The CDS features starting at the same coordinate suggest that the 5'UTR wasn't annotated for this gene. This is probably due to this gene being computationally predicted rather than annotated with biological evidence (Ie. RNA-seq). ...
written 9 weeks ago by Damian Kao15k
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Answer: A: Are there any de novo assemblers which can handle (either) transcriptomic or gen
... The two confounding factors that differentiates transcriptomic and genomic assemblies is read coverage and splicing. In a genomic assembly, you are assuming a relatively even coverage across your genome with spikes of higher coverage for repetitive/multi-copy regions. This coverage information can ...
written 10 weeks ago by Damian Kao15k

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Scholar 9 weeks ago, created an answer that has been accepted. For C: Does trinity discard reads shorter than 25-mer?
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Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: A Farewell To Bioinformatics
Popular Question 8 months ago, created a question with more than 1,000 views. For deseq2 user defined size factors
Popular Question 9 months ago, created a question with more than 1,000 views. For deseq2 user defined size factors
Appreciated 9 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Popular Question 9 months ago, created a question with more than 1,000 views. For deseq2 user defined size factors

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