User: brianpenghe

gravatar for brianpenghe
brianpenghe20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
3 weeks, 6 days ago
Joined:
5 years, 2 months ago
Email:
b**********@gmail.com

Posts by brianpenghe

<prev • 14 results • page 1 of 2 • next >
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Answer: A: Extracting last N bases of reads in FASTQ file
... To get an output in fastq format (say last 20 basepair) you have to do this: ``` paste <(cat my.fastq | paste - - | cut -f1 | tr "\t" "\n") <(cat my.fastq | paste - - | cut -f2 | tr "\t" "\n" | grep -o '.{20}$' ) | tr "\t" "\n" ``` ...
written 4 weeks ago by brianpenghe20
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Comment: C: Fastq Convert To Fasta
... The upsides: 1. it can do reads trimming at the same time, which is frequently required in small RNA fields 2. a functional command is short 3. it's in python But I have to admit that Irsan's answer is good enough. ...
written 4 months ago by brianpenghe20
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Answer: A: Fastq Convert To Fasta
... You can use [my script][1] [1]: https://github.com/brianpenghe/fastq-scripts/blob/master/fastqtofasta.py ...
written 4 months ago by brianpenghe20
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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 13 months 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 14 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 14 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 16 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 18 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 2.3 years ago by brianpenghe20 • updated 2.3 years ago by genomax80k
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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 4.1 years ago by brianpenghe20 • updated 4.1 years ago by Devon Ryan94k

Latest awards to brianpenghe

Popular Question 20 months ago, created a question with more than 1,000 views. For Why doesn't UCSC show mouse centromeres?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Difference between RepeatMasker and RepeatMasker viz.

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