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Request for demo data #3

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tenlives opened this issue Mar 28, 2024 · 2 comments
Open

Request for demo data #3

tenlives opened this issue Mar 28, 2024 · 2 comments

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@tenlives
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tenlives commented Mar 28, 2024

Hello,
It is a great tool to map barcode from stereo-seq to stereo-chip.
Could you provide demo data to us to benchmark our result?
The --barcodeStart in my file does not start at 0, so I set barcodeStart parameter in a particular value, I am not sure my result is right or not.

@liuxingnancy
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@tenlives
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tenlives commented Aug 11, 2024

Thanks very much!
I encountered another problem that when I run the procedure "ST_BarcodeMap-0.0.1 --in barcodeToPos.h5 --in1 read1.fq.gz --in2 read2.fq.gz --out read1_mapped.fq.gz --out2 read2_mapped.fq.gz --unmappedOut read1_unmapped.fq.gz --unmappedOut2 read2_unmapped.fq.gz --mismatch 1 --thread 10 --barcodeStart 36 --barcodeLen 25 --umiStart 76 --umiLen 10 --PEout", the output file read1_mapped.fq.gz contains the beginning 36bp of the reads, not the barcode region which I setted.
Could you help me to resolve it? Thank you!

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