Scripting and dealing with large datasets is an important skill to have as a biologist. For example, it is not uncommon to have expression data for 30,000 genes in a single file! Therefore, utilizing the command line is critical for quickly and efficiently making sense of your data. Below I have attached a couple of example BASH scripts that you may find useful. The first (gene_finder.sh) searches a file containing GeneIDS and annotations from your taxon of interest for all genes that you may be interested in and parses a larger table of gene counts into just those you specified. I recently used it to find all the ribosomal proteins in the oyster genome. The second processes output from DESeq and makes a separate file of JUST differentially expressed genes.
Finally, I have attached a third file (basic_UNIX_commands.txt) that contain various unix commands that may aid you in your own scripting. This contains commands that accomplish text manipulation examples to accompany the excellent book "Practical computing for biologists" by Steven Haddock and Casey Dunn. I highly recommend always keeping a commented list of commands handy as you play on the command line. Copying and pasting to these command lists will be a great start to your next script. Feel free to contact me with any questions of how to help with your coding and I will help if I can. Enjoy!
Finally, I have attached a third file (basic_UNIX_commands.txt) that contain various unix commands that may aid you in your own scripting. This contains commands that accomplish text manipulation examples to accompany the excellent book "Practical computing for biologists" by Steven Haddock and Casey Dunn. I highly recommend always keeping a commented list of commands handy as you play on the command line. Copying and pasting to these command lists will be a great start to your next script. Feel free to contact me with any questions of how to help with your coding and I will help if I can. Enjoy!

gene_finder.sh | |
File Size: | 2 kb |
File Type: | sh |

rnaseq_processing.sh | |
File Size: | 1 kb |
File Type: | sh |

basic_unix_commands.txt | |
File Size: | 6 kb |
File Type: | txt |