Question on Data access

joeb-liver / Single_Cell_Liver_Atlas

R code for metaanalysis of single cell liver data

GNU General Public License v3.0

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Question on Data access #1

Open biooo opened 3 years ago

biooo commented 3 years ago

Hi I got a chance to visit your website (http://liveratlas-vilarinholab.med.yale.edu/). It includes much useful information. Great work. Please may I ask how did you download the raw FASTQ sequencing files from GSE115469 as described in your webste. It seems the SRA achieve only contains one rather than three FASTQ files (e.g. https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR7276478). Or did you use bam file (that is not very raw). Many thanks.

Best wishes, Henry

joeb-liver commented 3 years ago

Hi Henry, You are correct that I unfortunately used the BAM files as they are all that were available. The BAM files were created as an were described as an output of Cellranger which is our normal processing pipeline in the Vilarinho lab anyway. Sorry for any confusion!

-Vilarinho Lab