Moderator: JC

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JC8.2k
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Computational Biologist

Posts by JC

<prev • 714 results • page 2 of 72 • next >
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Comment: C: Genome and DNA - whats the correlation
... Yes and no, some genes can be just a continuous region (like in virus or bacteria) and anything that falls inside can potentially break the gene. In eukaryotes, genes are more complex, it can be several exons than can span several kilobases (introns), inside introns you can have other genes, repetit ...
written 13 days ago by JC8.2k
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Comment: C: Genome and DNA - whats the correlation
... Yes and yes. Genome is all DNA which defines (and it's inherited by) an organism, so it includes everything, genes (coding and non-coding) and everything else (regulatory regions, pseudogenes, repetitive regions and "junk" DNA). The word is a combination of GENe and chromosOME. ...
written 14 days ago by JC8.2k
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Comment: C: Genome and DNA - whats the correlation
... No, that means that 98% of the genome is not encoding genes, only 2% and that is the 20,000 coding genes ...
written 15 days ago by JC8.2k
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Comment: C: Bioinformatician - Databiology Mexico
... The position is still open, feel free to send your CVs. ...
written 19 days ago by JC8.2k
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Answer: A: Can I compare TPM values for a transcript across different transcriptome assembl
... > I cannot find any literature or posts in regard to this, if you can point me to any resources You cannot because is not possible to compare expression between 2 different species, there are many biological factors that will affect your quantification even if this is normalized in TPM. The best ...
written 28 days ago by JC8.2k
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Answer: A: know the grep command for fastq file
... if the file is decompressed: `grep -A4 HISEQ:151:HHKH7BCXX:2:1203:18952:80029 file.fastq` if the file is compressed: `zgrep -A4 HISEQ:151:HHKH7BCXX:2:1203:18952:80029 file.fastq.gz` `man grep` can explain to you how to use it ...
written 4 weeks ago by JC8.2k
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Answer: A: i can't find the SRR sample on NCBI FTP, such as SRR018260
... A few weeks ago I have a similar case, so I reported to the NCBI staff who responded: > This location became unsustainable long time ago and is not maintained. New data were not added for years. > You need to use SRA Toolkit for downloading SRA data. Please refer to the Download guide: https: ...
written 6 weeks ago by JC8.2k
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Comment: C: Why do I have more than 5000 variants when I used a 5K snp array?
... You can have multiple cases, but mainly in individual calls you are also considering "personal" variants (only present in one individual), if you want something more complete, you can take a look into the Population calls in GATK https://software.broadinstitute.org/gatk/documentation/article.php?id= ...
written 8 weeks ago by JC8.2k
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Comment: C: Suspicious feature from 16S rRNA gene analysis using archaeal primers
... Blasting that with megablast don't have any significant hit, using blastn it gives the [short hits][1] that you described, so I guess is just contamination. [1]: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=H4P95KKS014 ...
written 8 weeks ago by JC8.2k
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Answer: A: Suspicious feature from 16S rRNA gene analysis using archaeal primers
... [Blasting][1] your sequence to NT, the best hit is a 16S from uncultured archaea (Score=641, Query cov=80%, E=6e-180, %identity=95.31%) [1]: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=H4N85R03014 ...
written 8 weeks ago by JC8.2k

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Teacher 4 days ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Scholar 4 days ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
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Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Programming Challenge - Synthetic Whole Genome Vcf
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Popular Question 11 weeks ago, created a question with more than 1,000 views. For Bioinformatician, Cellnetix Pathology And Laboratories, Seattle, Wa
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
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Teacher 7 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
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Scholar 9 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome

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