Luyi Tian

Sorry, I didn't keep the record. But I am sure it is in R 3.4 and early 2018. The spike-in mode works fine though. So I will still use that...

Hi, The file format is basically the same as a gene counting matrix from scRNAseq data, the only difference is that the first two colunms contain both gene id and...

you need paired-end read as input so two fastq file.

The separate functions are designed so scPipe can process bam file generated from Drop-seq tools and CellRanger, which also uses bam file and aux tag to store barcode and UMI....

this file changes for different dataset and is generated by cellranger by analysing matching short-read data. so you have to sequence the same cells using short-read to acquire this file.

yes. I don't have a clear overall design at first. I wrote the C++ part first as a stand-alone command line tools, and decide to build an R package, later....

FLAMES perform more aggressive filtering than flair and other tools so it is not surprised you get less isoforms. you can change the parameter here: "Min_sup_cnt":5, "Min_cnt_pct":0.001, "Min_sup_pct":0.2, like reduce...

for 1). I would recomment you try `config_sclr_nanopore_default.json` and change `"strand_specific":-1,` depending on your protocol. Normally if it is a bulk cDNA nanopore sequencing data then it wont be strand...

The nanopore sequencing protocol is not strand specific but the 10X single cell protocol is. if you use `match_cell_barcode` for barcode detection and trimming then the output should be in...

oh that is weird. the format for fastq read names should be @CellBarcode_UMI#OriginalName. so there should be only one cell barcode and UMI tag in the read name. can you...