Hi, I have to analyze published scRNA-Seq data. Data are Chromium 10X on NovaSeq6000 and: for each sample I have forward (R1) in lane1 and lane2 (and hence two files) and reverse (R2) in lane1 and lane2 (and hence two files). Totally I have 4 files for sample. I have .fastq files. I usually analyze 10X scRNA-Seq data using Cellranger in single strand starting from the demultiplexing and ending with the alignment. It is the first time I have forward and reverse fastq files on multiple lanes and I don't know how to analyse them. Can anyone give me some hints on the analysis I have to do? Suggestions on tutorials, tools, papers about my task are more than welcome.
Thank you in advance
2 answers
Just use cat to merge the R1s and the R2s respectively.
cat R1_lane1.fastq.gz R1_lane2.fastq.gz > R1.fastq.gz
same for R2.
See answer from swbarnes2 below, apparently CellRanger is picky about file names.
I am not a CellRanger user, I prefer lightweight approaches such as Alevin for scRNA-seq quantification and for this (and probably most other applications) cating is fine. A CellRanger-like approach that is faster and more generic (=less picky) would be STARsolo.
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Are you still planning to use
cellranger?No no it is the practice of the lab but it is not mandatory