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How to demultiplex a mix of single-indexed and dual-indexed samples
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+ Bioinformatics
+ Illumina
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Mark Timko
How to demultiplex a mix of single-indexed and dual-indexed samples
I'm late to the party but simply run cellranger mkfastq twice, with different arguments for the mask and with --filter-dual-index for the double-indexed samples. In a second step you then have to disentangle the dual A+B reads from single-index A reads based on the readID's that are found in both of the demultiplexings. This is cumbersome and time+diskspace consuming, but it can be done. I would use some Unix tools for that but there are probably smarter ways.
EDIT: I mistakenly said bcl2fastq, this must be cellranger mkfastq. (thanks AmadeusDrZaius)
I'm late to the party but simply run cellranger mkfastq twice, with different arguments for the mask and with --filter-dual-index for the double-indexed samples. In a second step you then have to disentangle the dual A+B reads from single-index A reads based on the readID's that are found in both of the demultiplexings. This is cumbersome and time+diskspace consuming, but it can be done. I would use some Unix tools for that but there are probably smarter ways.
EDIT: I mistakenly said bcl2fastq, this must be cellranger mkfastq. (thanks AmadeusDrZaius)
ah yes, that is true, sorry. I guess you would have to do an additional filtering step on the FASTQ file, the second word on the ID lines is 'index1+index2' for properly demultiplexed reads.More
I'm late to the party but simply run
cellranger mkfastqtwice, with different arguments for the mask and with--filter-dual-indexfor the double-indexed samples. In a second step you then have to disentangle the dual A+B reads from single-index A reads based on the readID's that are found in both of the demultiplexings. This is cumbersome and time+diskspace consuming, but it can be done. I would use some Unix tools for that but there are probably smarter ways.EDIT: I mistakenly said
bcl2fastq, this must becellranger mkfastq. (thanks AmadeusDrZaius)I'm late to the party but simply run
cellranger mkfastqtwice, with different arguments for the mask and with--filter-dual-indexfor the double-indexed samples. In a second step you then have to disentangle the dual A+B reads from single-index A reads based on the readID's that are found in both of the demultiplexings. This is cumbersome and time+diskspace consuming, but it can be done. I would use some Unix tools for that but there are probably smarter ways.EDIT: I mistakenly said
bcl2fastq, this must becellranger mkfastq. (thanks AmadeusDrZaius)More
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