R2 files missing?

[MelissaGall]

Hi,

I am trying to recover the SMARTseq files and run Kallisto but I am only able to download R1 files.

First, I ran this command line:

wget --continue --quiet -P ../../data/SMARTseq/fastqs/ -i ../../reference/smart-seq_file_links.txt

It returned an error message (404 not found). I guess this is because the location of the files changed. For example, http://data.nemoarchive.org/biccn/lab/zeng/transcriptome/scell/SMARTer/raw/MOp/LS-15395_S41_E1-50.fastq.tar seems to be now http://data.nemoarchive.org/biccn/lab/zeng/transcriptome/scell/SSv4/mouse/raw/MOp/LS-15395_S41_E1-50.fastq.tar. I changed the URL and was able to download the data.

But, when I run the script to un-tar the files, I have only R1 reads in the folder. Is this expected?

Ultimately, I will be interested in the matrix with isoform counts (so before grouping them together to get gene-level counts, if my understanding is correct), but I can't find it anywhere.

Could you help me? Sorry if I missed something!

Thank you! :)