Moderator: Damian Kao
Damian Kao ♦ 15k
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Bioinformatician at Janelia Research Campus.
Posts by Damian Kao
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... 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 ...
written 5 days ago by
Damian Kao ♦ 15k
• updated
5 days ago by
swbarnes2 ♦ 4.1k
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... Starcode is for UMI clustering, but it should also work for your purposes:
https://github.com/gui11aume/starcode ...
written 19 days ago by
Damian Kao ♦ 15k
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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 Kao ♦ 15k
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... 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 Kao ♦ 15k
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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 Kao ♦ 15k
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... 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 Kao ♦ 15k
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... 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 Kao ♦ 15k
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206
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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 Kao ♦ 15k
6
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... 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 Kao ♦ 15k
2
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130
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... 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 Kao ♦ 15k
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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?
Scholar
9 weeks ago,
created an answer that has been accepted.
For C: What's the correct way to withdraw a published database/server ?
Good Answer
9 weeks ago,
created an answer that was upvoted at least 5 times.
For A: A Farewell To Bioinformatics
Teacher
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created an answer with at least 3 up-votes.
For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Teacher
10 weeks ago,
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For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
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3 months ago,
created a question with more than 1,000 views.
For deseq2 user defined size factors
Commentator
4 months ago,
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For C: Shall We Go Back To Stackexchange?
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5 months ago,
created a post with more than 5 votes.
For A: A Farewell To Bioinformatics
Teacher
5 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
Teacher
6 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
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6 months ago,
created an answer that has been accepted.
For C: What's the correct way to withdraw a published database/server ?
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6 months ago,
created an answer that was upvoted at least 5 times.
For A: Bwa What Is In .Sai File
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For A: A Farewell To Bioinformatics
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For Given Unlimited Resources, What Would Be Your Dream Experiment?
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For A: A Farewell To Bioinformatics
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For deseq2 user defined size factors
Popular Question
8 months ago,
created a question with more than 1,000 views.
For deseq2 user defined size factors
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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