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pachterlab / kite

kallisto index tag extractor
BSD 2-Clause "Simplified" License
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Using kite for haircut-seq #9

Open abearab opened 3 years ago

abearab commented 3 years ago

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 commented 3 years ago

@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.