Question: Single cell RNA seq data set alignment
gravatar for ailin_leticia.buzzi
3 months ago by
ailin_leticia.buzzi0 wrote:


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.



rna-seq alignment • 243 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by ailin_leticia.buzzi0
gravatar for mtekman89
3 months ago by
mtekman8910 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 3 months ago by mtekman8910
gravatar for ailin_leticia.buzzi
3 months ago by
ailin_leticia.buzzi0 wrote:

Hello Mehmet, I have sequenced roughly 900 cells using Single cell Smart-Seq2 and Nextera XT library prep, which come from three different biological time points in the development of the inner ear of the chick embryo. Approximately 600 of them where then sequenced using HiSeq4000, 75 PE and the rest HiSeq4000 75bp SE (as these were 2 separate experiments done with one year gap).

I would first like to know which options you have to set up the alignment of my data set which would include adapter trimming, alignment to Galgal5 (as my samples come from Gallus gallus), and processing to obtain the read counts matrix of the 900 cells.

I am very happy to hear that you're also setting up clustering pipelines. My main interest is to establish trajectories to understand how my population of interest is making fate choices.

I would be really happy to try your pipeline as soon as the workflow is available on Galaxy. Please, let me know if you need further information. Best,


ADD COMMENTlink written 3 months ago by ailin_leticia.buzzi0
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