Question: Questions about Alignment and downstream workflow for scRNA-Seq Data
gravatar for rajeev.vikram
20 months ago by
rajeev.vikram30 wrote:


I am new to single cell (SC) RNA-Seq and have a rather naive q regarding the alignment of single cell fast q files. As, there are hundreds/thousands of fast q files corresponding to their respective SCs, How do we align all these fastq files in parallel? should one align a few fastq files at a time or all these (hundreds/thousands of fast q files) all at once in some aligner? (Hisat/STAR). What is the preferred method? Is there any online instruction available regarding this (I didn't find anything addressing this specifically, that why I think its probably too naive) I am fairly conversant with bulk sequencing methods so any link to a fairly basic but recent workflow would be a great help.

PS: I am working with about 4k publicly available cancer single cell fast q files.


ADD COMMENTlink modified 20 months ago by Devon Ryan92k • written 20 months ago by rajeev.vikram30

Are you sure your technique will result in a separate file for each cell? Many techniques do not.

ADD REPLYlink written 20 months ago by swbarnes26.9k

I was talking from a bulk-seq perspective, where we have one(or two) fastq files per sample. I am not really aware of how scRNA-Seq works, probably in batches, but how, thats why I asked the question. An example would be great.

ADD REPLYlink written 20 months ago by rajeev.vikram30
gravatar for Devon Ryan
20 months ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

STAR is actually pretty convenient, in that you can have it load the index into memory and leave it there for multiple alignment runs. That ends up saving a couple minutes per run, which, given the low sequencing depth of individual cells, can add up to a serious performance increase. My suggestion would be to see if you can use STAR is this manner with however you create your workflows.

ADD COMMENTlink written 20 months ago by Devon Ryan92k
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