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Building the cDNA intron index #2

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achamess opened this issue Sep 20, 2019 · 0 comments
Open

Building the cDNA intron index #2

achamess opened this issue Sep 20, 2019 · 0 comments

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@achamess
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I am trying to follow the tutorial to build a cDNA intron index for single nucleus data processing on 10x.

I am following the steps to generate the BED file, but I am not sure where to input the information for the flank size.

Here is what I see on UCSC browser when following the instructions:

Screen Shot 2019-09-20 at 12 28 22 PM

Where should I put the L-1 flank?

Also, regarding the input FASTQ files, these are the files that come out after I've run mkfastq in CellRanger, yes?

Thanks!
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@achamess