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News: Variant Analysis, Bioinformatics Prerequisites, & Genome Browser workshops at UC Davis

class news training workshop written 3 months ago by nikhil.ashok.joshi • 10

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Parsing FASTA file using class in Python

fasta python class biopython parsing written 19 months ago by mrth • 30 • updated 19 months ago by Matt Shirley ♦ 8.6k

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Tutorial: Scripting for Biology - Online Virtual Classroom-based Module

perl python class tutorial go written 3.1 years ago by ugly.betty77 • 1.0k

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Recent Replies

A: How to reformat (i.e. to clean) NCBI .fasta archives into a singleline .fasta wi by Jung Soh • 0
A solution using the [seqtk][1] toolkit: seqtk seq -Cl0 in.fasta > out.fasta The `-C` opt...
C: Conda on MacOS by steve • 1.7k
why are you using `curl` instead of the `wget` command you posted?
C: How can I make a .bed file from my fasta? by steve • 1.7k
It sounds like your trouble is in the bamtobed step. I would focus on troubleshooting that. Might...
C: How do I modify default ggplot2 axis? by jaqx008 • 40
Thanks Guys. It works now but without the p. I appreciate it. :)
C: How do I modify default ggplot2 axis? by Medhat ♦ 7.9k
let p -> ggplot(DE, aes(x = DE$V2, y = DE$V3, color = DE$V8, pch = DE$V7 > .05)) + ge...
C: How do I modify default ggplot2 axis? by jaqx008 • 40
Where in the code could this fit in? thanks Ive tried adding the limits but not sure were it shou...
C: Faster way to get sequences from large fasta files? by Pierre Lindenbaum ♦ 113k
If an answer was helpful you should upvote it, if the answer resolved your question you should ma...
A: How do I modify default ggplot2 axis? by rjactonspsfcf • 70
just add limits + xlim(-5,5) + ylim(-5,5) see: https://ggplot2.tidyverse.org/reference/lim...
C: What are the recommended methods for merging de-novo assemblies? by jrj.healey ♦ 7.7k
If you’re not looking to close the assemblies, and the contigs pass reasonable quality control, y...
C: Sorting fq data into groups with missing barcode info? by jorja • 0
These are the data I got and that basically this is it... My guess is like your guess that they a...
C: Sorting fq data into groups with missing barcode info? by jorja • 0
Super! That is very nice to know. Thank you, Albert! I will do it this way then!
C: What are the recommended methods for merging de-novo assemblies? by Damian Kao ♦ 15k
So you have 88 sets of metagenomic reads? I don't see why not just merge them all and treat them ...

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