Moderator: Damian Kao

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Damian Kao14k
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Website:
http://blog.nextgeneti...
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6 years, 7 months ago
Email:
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Bioinformatician at Janelia Research Campus.

Posts by Damian Kao

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Comment: C: Jellyfish: every other kmer count is zero
... 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 22 days ago by Damian Kao14k
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Comment: C: R or python, which one do you prefer in analysing scRNAseq datasets?
... 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 5 weeks ago by Damian Kao14k
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Comment: C: pyncls not dead! The datastructure nested containment list (faster than interval
... I think it's supposed to be faster for short intervals? ...
written 6 weeks ago by Damian Kao14k
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Comment: C: Using rna-STAR on Amazon EC2 instance
... From what I know, the shared memory feature is used so multiple separate STAR jobs can access the same loaded genome index. So if you have relatively small amount of memory and you want to run multiple jobs, this will reduce your memory footprint. How many separate STAR jobs are you running? Your p ...
written 8 weeks ago by Damian Kao14k
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Comment: C: Hybrid assembly using MinION data + correction with Illumina. Which strategy to
... Try all of them. In my experience there isn't one method that just works all the time. Sometimes my Spades is better than my Canu. Sometimes my miniasm is better than my Spades,etc. ...
written 8 weeks ago by Damian Kao14k
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Comment: C: using awk to extract a specific pattern
... Have you tried the -y parameter in gffread: -y write a protein fasta file with the translation of CDS for each record ...
written 8 weeks ago by Damian Kao14k
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Comment: C: using awk to extract a specific pattern
... Your file looks like a gtf file, not gff. And you probably want to be careful with what you mean by "first" CDS. Do you mean "first" according to genomic coordinate or "first" according to the gene? If a gene is on the minus strand of the genome, the first CDS according to the gene is actually the l ...
written 8 weeks ago by Damian Kao14k
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Answer: A: How to get the total genic and intergenic length of a chromosome?
... It looks like you have a .gtf file. That means you can extract the exon lines from the .gtf file and count and sum up the exonic intervals. You can generate a sorted .bed file of exon coordinates by: grep -P '\texon\t' your.gtf | cut -f 1,4,5 | sort -k1,1 -k2,2n > exons.bed You can merge t ...
written 8 weeks ago by Damian Kao14k
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Answer: A: long-range technologies for genome scaffolding
... I recently got back a genome from Dovetail that increased N50 from ~100kb to ~50MB. Yes, that's a 500X increase in contiguity. N50 should not be the only stat for assessing how good a genome is. But it is still pretty impressive. Gene discovery/BUSCO stats also significantly increased. A few cavea ...
written 10 weeks ago by Damian Kao14k
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Comment: C: Variant calling in genomic chunks
... Thanks for the reply. I see what you mean with the SVs and possibly even indels. I am not interested in SVs for now, but do want to preserve indel information if I can. The BAM files I am working with are low coverage. I guess I'll to write a script to chunk the BAM file based on coverage "islands ...
written 10 weeks ago by Damian Kao14k

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Commentator 22 days ago, created a comment with at least 3 up-votes. For C: Shall We Go Back To Stackexchange?
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 8 weeks 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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