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pachterlab / kallistobustools

kallisto | bustools workflow for pre-processing single-cell RNA-seq data
https://kallistobus.tools/
MIT License
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kallistobus for MARSseq data #13

Closed ogandril closed 4 years ago

ogandril commented 4 years ago

Dear authors In the actual version of kallistobus, the -x Technology argument does not incorporates MARSseq technology. Any chance this might be implemented soon? If not, how challenging would that be to implement a -x MARSseq argument? Best Olivier

gaofan83 commented 4 years ago

Hi Olivier, Please take a look at https://pachterlab.github.io/kallisto/manual. If you know the positions of bc, umi and feature, you should be able to use -x argument.

"Additionally kallisto bus will accept a string specifying a new technology in the format of bc:umi:seq where each of bc,umi and seq are a triplet of integers separated by a comma, denoting the file index, start and stop of the sequence used. For example to specify the 10xV2 technology we would use 0,0,16:0,16,26:1,0,0. The first part bc is 0,0,16 indicating it is in the 0-th file (also known as the first file in plain english), the barcode starts at the 0-th bp and ends at the 16-th bp in the sequence (i.e. 16bp barcode), the UMI is similarly in the same file, right after the barcode in position 16-26 (a 10bp UMI), finally the sequence is in a separate file, starts at 0 and ends at 0 (in this case stopping at 0 means there is no limit, we use the entire sequence)."

ogandril commented 4 years ago

Dear Fan

Thank’s a LOT. Very helpful.

Best

Olivier

Le 12 juil. 2020 à 22:24, Fan Gao notifications@github.com a écrit :

Hi Olivier, Please take a look at https://pachterlab.github.io/kallisto/manual https://pachterlab.github.io/kallisto/manual. If you know the positions of bc, umi and feature, you should be able to use -x argument.

"Additionally kallisto bus will accept a string specifying a new technology in the format of bc:umi:seq where each of bc,umi and seq are a triplet of integers separated by a comma, denoting the file index, start and stop of the sequence used. For example to specify the 10xV2 technology we would use 0,0,16:0,16,26:1,0,0. The first part bc is 0,0,16 indicating it is in the 0-th file (also known as the first file in plain english), the barcode starts at the 0-th bp and ends at the 16-th bp in the sequence (i.e. 16bp barcode), the UMI is similarly in the same file, right after the barcode in position 16-26 (a 10bp UMI), finally the sequence is in a separate file, starts at 0 and ends at 0 (in this case stopping at 0 means there is no limit, we use the entire sequence)."

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gaofan83 commented 4 years ago

You are welcome.