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Trying to align fastq files - UMI barcode position #4

Open bweatherbee opened 3 years ago

bweatherbee commented 3 years ago

Hello. I am currently trying to realign the raw data from this paper using the kallisto-bustools pipeline. I am able to specify custom technology by demarcating which read and the start and end position of the barcode and UMI. However, when I am trying to align it, the output is not giving the outcome of barcodes expected based on the deposited .txt files. Can you clarify the formating of the files and position of the barcode and UMI in them?

WRui commented 3 years ago

The 8nt cell barcode located at the beginning of Read 2. Following the barcode, it's 8nt UMI sequence. Associated code have been uploaded to the GitHub (https://github.com/WRui/Post_Implantation/tree/master/scRNA_UMI ), the barcode sequences and corresponding sample names can be found in the XXX.Info file. Running the code in Split_Barcodes to split data and perform QC process. For the convenvience of subsequent analysis, we add the suquence of cell barcode to read name during the QC process.

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From: bweatherbee Date: 2020-08-13 05:03 To: WRui/Post_Implantation CC: Subscribed Subject: [WRui/Post_Implantation] Trying to align fastq files - UMI barcode position (#4) Hello. I am currently trying to realign the raw data from this paper using the kallisto-bustools pipeline. I am able to specify custom technology by demarcating which read and the start and end position of the barcode and UMI. However, when I am trying to align it, the output is not giving the outcome of barcodes expected based on the deposited .txt files. Can you clarify the formating of the files and position of the barcode and UMI in them? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

gdevt commented 3 weeks ago

The 8nt cell barcode located at the beginning of Read 2. Following the barcode, it's 8nt UMI sequence. Associated code have been uploaded to the GitHub (https://github.com/WRui/Post_Implantation/tree/master/scRNA_UMI ), the barcode sequences and corresponding sample names can be found in the XXX.Info file.

Hello WRui, thank you for your analysis! Where can I find the cell barcodes for all samples / patients to provide to the script as XXX.Info? Looking at the repository that is linked, I only see Test.Info which seems to contain only a subset for P12 (for testing I assume).