Description
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
-kequal to the length of the Feature Barcodes
So, I must set-kto 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