search

yuntianf / Longcell-pre

Preprocessing for single cell/Visium Nanopore long reads sequencing to generate isoform quantification
3 stars 2 forks source link

how to acquire Nanopore fastq/bam data #4

Open LilyLuyang opened 4 months ago

LilyLuyang commented 4 months ago

Hi yuntian,

Thanks for this very useful tool for the single cell isoform data preprocessing and downstream analysis!

I couldn't find fastq sequencing data from the paper, so could you please share Nanopore sequencing data so that I could learn how to do preprocessing using Longcell-pre pipeline? Thanks a lot! I would appreciate it very much.

Lily

yuntianf commented 4 months ago

Hi Lily, We haven't released our raw data as our paper is still under revision. But in the data folder I put a demo.bam as an example data to test. Currently I'm wrapping up the Longcell-pre into a new R package and anticipate to release it this or the next week. I would recommend to use the new one which is easier to install and use.

Best, Yuntian

LilyLuyang commented 4 months ago

Hi Yuntian,

Many thanks for your quick response! Yeah, I have found demo.bam here. That would be great if using this new R package!

Best, Lily