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BUStools / bustools

Tools for working with BUS files
https://bustools.github.io/
BSD 2-Clause "Simplified" License
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Understanding output.bus returned from kallistobustools #76

Open ahmadalajami opened 2 years ago

ahmadalajami commented 2 years ago

Hi,

I am using kallistobustools, namely kb ref and kb count commands to build the count matrix of a scRNA-seq dataset.

I have ran bustools sort and bustools text on output.filtered.bus in order to look at the alignments like the following: bustools sort -o output_sorted.bus output.filtered.bus bustools text -o output_sorted.txt output_sorted.bus

In your BUS-format repo, you describe the output as 5 columns named barcode, umi, ec, count, flags. However, my output only has 4.

  1. Why is that the case?
  2. Which information is stored in each column of my output?

output_sorted.txt looks like the following: AAATCCTGTAAACGTACCAATTACCGG AAAAAACA 93002 3 AAATCCTGTAAACGTACCAATTACCGG AAAAAAGA 1049056 1

Thank you in advance!

Yenaled commented 2 years ago

The order of columns is: barcode, UMI, ec, count

The flag column is not displayed by default (you can display it via the -f option)