Bioinformatics with Python Tutorial!! | Base Call

[@OMGenomics]

A quick tip when you find yourself opening something in Excel just to format data: There are usually better ways to do it that are actually easier. Here are 3 ways that are more reproducible: 1. `samtools depth -H reads.bam`. Yup, samtools depth actually has a flag for adding the header. Use --help on any tool to find such useful parameters. 2. `df = pd.read_csv('raw_depth.tsv', sep='\t', names=['chromosome', 'position', 'depth'])`. 3. If neither the input nor output tools can adapt, then you can use bash or python to format the data. For example: To make it comma-separated: `samtools depth reads.bam | tr '\t' ',' `. To add a header with awk: `cat depth.csv | awk 'NR==1{print "chromosome,position,depth"}{print}'`. So always look for ways the tool outputting the file can help format it, ways the input file can take in the input as-is, and finally ways to make the change programmatically without manual editing. Okay so that became longer than a quick tip, but hopefully this helps!

[@BaseCalling]

This is very helpful thank you!

[@jeffk8900]

Thanks!

[@islamsalah4314]

Just Wonderful... We need more.

[@whatthefilm3080]

Damn! Waiting for that!

[@shubol5839]

this content is so very important, thank you so much for this

[@ahmeddiab4372]

Amazing.

[@samuelfafiolu4198]

Hello sir, I have been following you for a while now, ever since i got admission to study MS Bioinformatics in the UK. You really did inspire me to go for it. I want to know where to really start from as I am new to this field. I would also love to know if I can connect for Mentorship. I love the field and would like to give it my best through proper guidance. I'd love to hear from you.

[@AbhiRavi-mf9xe]

Hi, love the videos on bioinformatics! Saw that AWS Omics just released, have you used it yet? If so, what are your thoughts on it?

[@muhammednagas6311]

thanks a lot

[@cheyukuo6068]

Hi, I’m a beginner and I was trying to turn the file from cram into bam but it kept saying chr is not presenting, how could I solve that?

[@cat_says_meow_meow_meow]

Hello! I have the same problem, have you found a solution?