Smart-seq2 data analysis

I have downloaded FASTQ files from a single cell experiment that used SMART-seq2. As you know, this pipeline generates 2 read files per single cell. I am able to allign the reads using HISAT2, however, I am not sure about the appropriate tool to merge the different counts together and produce a single cell matrix.
Any advice?
Thank you.

Hi @btilouche

These are our available tutorials for single-cell analysis. Not all tools are covered but maybe helps you to get oriented? Most are mapping some external publication or original author resources to the Galaxy version’s of tools, along with general text manipulations tools for intermediate steps (shell tools, etc). Those can be a reference for the “how-to” when custom translating methods from other sources, or when developing your own.

Maybe it is too late but still, this answer might help.

First, create a collection of FASTQs (paired collection in case of paired-end data). Then use Extract element identifiers of a list collection tool to extract the cell ids ( these are based on FASTQ names in the collection). Then use RNA STARSolo tool with Type of single-cell RNA-seq as Smart-Seq. Then select the FASTQ collection and extracted IDs as inputs. Please also check the other parameters carefully before running. This might take a while to finish. Hence, I suggest you to subsample your FASTQs before running on the whole datasets.

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