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danshu avatar danshu commented on September 28, 2024

I have a few questions after reading the help information.
For the requirement of BAM alignment files,
" NOTE: alignments must be sorted in order of name
index must be included in read name in the format read1_indexA
read name must include a number"
Do you mean sort the alignment in order of read name or reference name?
Index is the the 10X barcode string of the form 'ACGTACGTACGTAC-1'?
What does "read name must include a number" mean?

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warrenlr avatar warrenlr commented on September 28, 2024

please follow the instructions at:
ftp://ftp.bcgsc.ca/supplementary/ARCS/docs
and
ftp://ftp.bcgsc.ca/supplementary/ARCS/docs/arcsDemoScripts/readme.md

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danshu avatar danshu commented on September 28, 2024

Thanks for your help!

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