Question: Single cell RNA seq data set alignment
0
gravatar for ailin_leticia.buzzi
6 days ago by
ailin_leticia.buzzi0 wrote:

Hello,

I have a single cell RNA seq data (600 cells) and I would like to see the possibility to use Galaxy to analyze it. I understand the main purpose of galaxy is for bulk data, but since the alignment process is essentially the same, I thought you might had an option to make things more automatic for large data sets.

I would appreciate if you could let me know which options you have available, and also I understand I would need to increase my quota to be able to process this data set (at least for a short period of time until I get the read counts).

Looking forward to hearing from you.

Regards,

Ailin.-

rna-seq alignment • 45 views
ADD COMMENTlink modified 5 days ago by mtekman890 • written 6 days ago by ailin_leticia.buzzi0
0
gravatar for mtekman89
5 days ago by
mtekman890
mtekman890 wrote:

Hi Ailin,

I am currently in the process of implementing a scRNA pre-processing workflow (demultiplexing + alignment + quantification) in Galaxy, and am 99% complete. This workflow at the moment only works for single batches, with plans to extend it to handle multiple batches in one go -- however, it is mostly useable, just not public yet until the Galaxy tutorial for it is complete.

The workflow should be flexible enough to handle your data, but without the tutorial it may be somewhat indecipherable in terms of required inputs. Can I ask what capture/sequencing platform you are using?

In terms of clustering analysis, several downstream analysis workflows are also being developed at the moment; Scater/SC3-based, RaceID-based, and plans for a Seurat-based analysis. Currently RaceID2 has been implemented, but it is also in the process of being upgraded.

Best, Mehmet

ADD COMMENTlink written 5 days ago by mtekman890
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