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-   -   Single Cell RNASeq- Help (http://seqanswers.com/forums/showthread.php?t=90803)

rammohanshukla 09-06-2019 10:09 PM

Single Cell RNASeq- Help
 
Hi Experts,

I am new to single-cell analysis and am facing problem in getting the right pipeline to analyse a dataset from geo (Link : https://www.ncbi.nlm.nih.gov/geo/que...?acc=GSE116470 )

1) I want to download all files associated with Cerebellum and perform the analysis. any suggestions/pipeline to use these data will be very useful

GSM3239579 Cerebellum [P60CBRep1P1]
GSM3239580 Cerebellum [P60CBRep1P2]
GSM3239581 Cerebellum [P60CBRep1P3]
GSM3239582 Cerebellum [P60CBRep2P1]
GSM3239583 Cerebellum [P60CBRep2P2]
GSM3239584 Cerebellum [P60CBRep3P1]
GSM3239585 Cerebellum [P60CBRep3P2]

2) I see that there are other files available which include the row as gene names and columns as cells (see below in the same link as above with the file name: "GSE116470_F_GRCm38.81.P60Cerebellum_ALT.raw.dge.txt.gz")

Is there a way I can upload this file directly and start the analysis? I am hoping that working with the GSE116470_F_GRCm38.81.P60Cerebellum_ALT.raw.dge.txt data set will be easier than working with the GSM file.

Thanks in advance.

R


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