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How to run Monopogen gremlin on R2 of 10x fastq #82

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amirshams84 opened this issue Oct 14, 2024 · 1 comment
Open

How to run Monopogen gremlin on R2 of 10x fastq #82

amirshams84 opened this issue Oct 14, 2024 · 1 comment

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@amirshams84
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Hi I have list of 10X SingleCell data which R1 are missing from fastq files,
is there any way than we can align the R2 only using star and then feed bam file to monopogen germline
Thanks
should I use specific parameters during alignment /monopogen

Thanks
@jinzhuangdou
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Monopogen is highly flexible regarding read alignment. I believe you can proceed with that, but please ensure that the cell barcode is included in your aligned BAM files (with the CB flag).

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@amirshams84 @jinzhuangdou