Moderator: Damian Kao
Damian Kao ♦ 15k
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Bioinformatician at Janelia Research Campus.
Posts by Damian Kao
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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 2 days 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 2 days 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 3 days ago by
Damian Kao ♦ 15k
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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 3 days ago by
Damian Kao ♦ 15k
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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 10 days ago by
Damian Kao ♦ 15k
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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 17 days ago by
Damian Kao ♦ 15k
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... You can't calculate a p-value with no replicates as there is no measure of variance among your samples.
Best you can do is to filter out genes very stringently based on absolute read counts and then pick genes with high fold-changes.
...
written 17 days ago by
Damian Kao ♦ 15k
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... You also have no k-mers with frequency of 1, which is extremely unlikely. Did you somehow doubled up your input fastq? Did you copy the original fastq at some point and concatenated the copy to the original? ...
written 11 weeks ago by
Damian Kao ♦ 15k
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... Your bottle-neck is likely not going to be the choice of language. It's going to be the availability of existing packages to do what you want to do. Python will likely be faster for loading large datasets, but if there aren't already packages for scRNA-seq analysis, are you going to spend the time t ...
written 3 months ago by
Damian Kao ♦ 15k
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225
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... I think it's supposed to be faster for short intervals? ...
written 3 months ago by
Damian Kao ♦ 15k
Latest awards to Damian Kao
Scholar
10 days ago,
created an answer that has been accepted.
For C: Does trinity discard reads shorter than 25-mer?
Scholar
10 days ago,
created an answer that has been accepted.
For C: What's the correct way to withdraw a published database/server ?
Good Answer
10 days ago,
created an answer that was upvoted at least 5 times.
For A: A Farewell To Bioinformatics
Teacher
10 days 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
17 days 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
5 weeks ago,
created a question with more than 1,000 views.
For deseq2 user defined size factors
Commentator
11 weeks ago,
created a comment with at least 3 up-votes.
For C: Shall We Go Back To Stackexchange?
Appreciated
3 months ago,
created a post with more than 5 votes.
For A: A Farewell To Bioinformatics
Teacher
3 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
4 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
Scholar
4 months ago,
created an answer that has been accepted.
For C: What's the correct way to withdraw a published database/server ?
Good Answer
4 months ago,
created an answer that was upvoted at least 5 times.
For A: Bwa What Is In .Sai File
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4 months ago,
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For A: A Farewell To Bioinformatics
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5 months ago,
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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
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6 months ago,
created a question with more than 1,000 views.
For deseq2 user defined size factors
Good Answer
6 months ago,
created an answer that was upvoted at least 5 times.
For A: A Farewell To Bioinformatics
Popular Question
6 months ago,
created a question with more than 1,000 views.
For deseq2 user defined size factors
Popular Question
7 months ago,
created a question with more than 1,000 views.
For deseq2 user defined size factors
Appreciated
7 months ago,
created a post with more than 5 votes.
For A: A Farewell To Bioinformatics
Teacher
7 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
7 months ago,
created a question with more than 1,000 views.
For deseq2 user defined size factors
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