8000 Using kite for haircut-seq · Issue #9 · pachterlab/kite · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

Using kite for haircut-seq #9

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Open
abearab opened this issue Mar 17, 2021 · 1 comment
Open

Using kite for haircut-seq #9

abearab opened this issue Mar 17, 2021 · 1 comment

Comments

@abearab
Copy link
abearab commented Mar 17, 2021

Dear Pachter Lab members,

There is a single-cell method named haircut-seq which I'm trying to reimplement their pipeline using kallisto | bustools. I found kite the right tool for this purpose. They’ve introduced hairpin sequences. According to my understanding from the paper context and the Snakemake pipeline to count functional data, I was exploring to make this work.

Firstly, I have converted the above-mentioned fasta file to csv and then, I could basically run featuremap.py as you explained. Then, you described:

Build the kallisto index using the mismatch fasta and a k-mer length -k equal to the length of the Feature Barcodes
So, I must set -k to 63 while hairpins sequence lengths are 63. But, I got an error and I'm not sure what is the right way to overcome this problem.

Error: invalid k-mer length 63, minimum is 3 and maximum is 31

I appreciate it if you can give me some hints on this matter.

Thanks
@abearab
Copy link
Author
abearab commented Mar 17, 2021

@mandylr recently helped me by having access to the hairpin sequences (when I opened this issue. She might be able to participate in this conversation that could, at least, help me understand the concepts here. I could not follow the main commands for processing bam files while she wrote them in C++ and tbh, I don't have enough knowledge to understand that.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@abearab
0