User: brianpenghe

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brianpenghe20
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20
Status:
New User
Location:
United States
Last seen:
2 months, 3 weeks ago
Joined:
4 years, 4 months ago
Email:
b**********@gmail.com

Posts by brianpenghe

<prev • 11 results • page 1 of 2 • next >
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Answer: A: How To Extract Scores From Bedgraph File Using Bed Tools
... There are so many issues in the methods suggested above. A. different regions have different lengths. B. you don't know whether the "score" of inputs are already average scores of the region or the sum C. empty regions handling I'd suggest converting the bedgraph files into bigWigs and then using ...
written 12 weeks ago by brianpenghe20
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Answer: A: Converting TPM to FPKM
... It is always harder to convert TPM back to FPKM because TPM lost information that FPKM still contains. If you really want to do that, you have to find the normalizing constant, i.e., the ratio between FPKM and TPM since these two values are proportional to each other in the same sample. I'd suggest ...
written 3 months ago by brianpenghe20
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Comment: C: Converting TPM to FPKM
... There are benefits of FPKM to TPM. FPKM values of the same gene between different samples are proportional to RPM values of that gene, which is very useful for RPM believers, who value more about the mass of a massenger than the molar concentration when comparing different samples. TPM isn't superio ...
written 3 months ago by brianpenghe20
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Comment: C: Filtering Fastq Sequences Based On Lengths
... One note: This command doesn't work when the read names contain spaces. better use awk -F"\t" instead of awk ...
written 6 months ago by brianpenghe20
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Comment: C: Download Rrna Sequences
... That's indeed the best solution. One thing to add: to download sequences you gotta click on the attribute and select sequence instead of regions. ...
written 7 months ago by brianpenghe20
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Comment: A: bedtools coverage gives error received illegal bin number, but that number isn't
... I got the same error and the cause was a little bit different: In the bed file I downloaded there were lines with third column missing! chr1 3139719 chr1 12645719 chr1 12959919 chr1 14960519 chr1 24616961 chr1 24808855 chr1 26688455 chr1 3399 ...
written 17 months ago by brianpenghe20 • updated 17 months ago by genomax67k
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Why doesn't UCSC show mouse centromeres?
... Human genomes' centromeres are labeled with red arrows. However I can't find this type of labels in the mouse genome. Is there a way to show centromeres on the UCSC genome browser for mouse, too? ...
ucsc genome browser centromere written 3.2 years ago by brianpenghe20 • updated 3.2 years ago by Devon Ryan90k
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Comment: C: How To Combine Multiple Wig/Bigwig Files Into One
... I was wondering why they were using -clip. But your answer seems to suggest that -clip is not necessary ...
written 3.4 years ago by brianpenghe20
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Difference between RepeatMasker and RepeatMasker viz.
... I was trying to download a repeatMasker track from UCSC. However there are two options for mm10 genome: RepeatMasker and RepeatMasker Viz. Does anyone know the difference between them?     ...
repeat repeatmasker written 3.5 years ago by brianpenghe20 • updated 3.5 years ago by Dan500
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Answer: A: mm9 gene names to mm10
... You can get the mm9 coordinates of the genes, then use this https://genome.ucsc.edu/cgi-bin/hgLiftOver to convert the coordinates to mm10 and then get the annotations from there ...
written 3.5 years ago by brianpenghe20

Latest awards to brianpenghe

Popular Question 10 months ago, created a question with more than 1,000 views. For Why doesn't UCSC show mouse centromeres?
Popular Question 17 months ago, created a question with more than 1,000 views. For Difference between RepeatMasker and RepeatMasker viz.

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