UCSC table browser is a great tool that can be used to download different annotation data such as exon, intron, 5’ UTR, 3’ UTR etc. Here is an example to extract the exons from human genome versio...
Download links for public data and tools
This posts mainly consists of the links to different genomic data. UCSC Data links UCSC hg19 ftp site hg19 fasta liftover chain files phastcon 100 way score phylop 100 way score multi ...
Identify the strandedness of RNA Seq Data
Depending on the library preparation method, the RNA Seq data can be stranded or non-stranded. Here, is the link from Azenta, to better understand stranded vs non-stranded library preparation. Here...
Finding closest gene to the given genomic region
To find the closest gene to the given genomic region, we will be using bedtools closest. Fist lets see our region of interest $ cat input_region.bed chr16 566689 566964 id . + $ head -n 8 gencode...
Pandas Tricks
Splitting a row into multiple rows based on substring in a specific column Here I have a dataframe with 3 columns (p1, p2 and tissue). In column p2 I have 2 genes separated by ';' import pandas a...
Cheat Sheet
Linux Linux Cheat Sheet Git Github Cheat Sheet Conda Conda Cheat Sheet
Add frequency count for each category on box plot
Here I will show how to add frequency count to the each category in the box plot. For this we will use the searborn provided example dataset. First, lets load the dataset: import searborn as sns ...
Generate Motif Sequence From Pwm Matrix
I am using PWM (Position Weight Matrix) file in meme format downloaded from JASPAR database as the input file. I am using random.choices from python to randomly generate the nucleotide motif sequen...
Creating Multiple Subplots in One Figure Using Seaborn Python
If you want to include multiple plots in a single figure, you can do that by creating axes. Here, is the sample code for that. In this section of code I am just loading the example dataset. impor...