software of single-cell RNA-seq from fastq or fasta

Question

[yueli7]

Hello,

Anyone know which software or pipeline can treat the single-cell RNA-seq data from the first beginning? That means from the form of single or pair-end reads, and barcode, not matrix? The output should be tabulate reads and ready use for Seurat.

Thanks in advance for great help!

Best,

Yue

[GenoMax]

It would be beneficial to add what kind of single-cell data you have? There are a few different platforms/types and the raw data is not as simple as single/paired fastq files.

[yueli7]

Thanks, genomax,

I will add to that.

[GenoMax]

single or pair-end reads, and barcode

Cellranger demultiplexed data is like that. Two read files and a separate file for index reads. You could just use cellranger counts (links provided in other answers). alevin (link) would also be a good solution.

[yueli7]

Hello, genomax,

Thank you so much for your great help!

Best,

Yue

Answer 1

[swbarnes2]

10XGenomics cellranger will take fastqs as input and output files that Seurat can take.

But then your fastq files have to be compatible with what cellranger is expecting, which any other kind of platform won't be without a lot of futzing and trickery.

Most platforms come with scripts that will process the data for you, and they are customized for data files of their type.

[yueli7]

Hello, swbarnes,

Thank you so much for your great help!

Best,

Yue

Answer 2

[bioinformatics2020]

I'm a little confused by your question. So you're looking for software that will take your raw single-cell FASTQ and create a file that can be fed into Seurat? If so, this depends on which company did the sequencing. If it was 10XGenomics, they have software called Cell Ranger that'll take your raw FASTQ files, and turn it into a matrix that can be read by Seurat (using the Read10X function.)

[yueli7]

Hello, bioinformatics2020

Thank you so much for your great help!

Best,

Yue

Answer 3

[Ömer An]

Hi,

You can use scRNA-Seq pipeline for 10x samples on CSI NGS Portal starting from fastq files all the way to the matrix folder that Seurat can read as the input. Everything is fully automated.

[yueli7]

Hello, Omer An,

Thank you so much for your responding!

Thank you!

Best,

Yue