9 votes
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What is the index fastq file (sample_I*.fastq.gz) generated when demultiplexing Illumina paired-end runs?

tldr - The I*.fastq.gz file contains the read index sequences. long explanation Illumina uses a program called bcl2fastq to demultiplex sequencing runs. This ...
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3 votes

Demultiplex nanopore reads with custom barcodes

There are two other ways in which you could demultiplex reads if guppy doesn't have the config file for the kit you are using. Minibar: This works for dual index barcodes specifically Porechop: This ...
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3 votes
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Demultiplex nanopore reads with custom barcodes

My semi-automatic workflow for demultiplexing nanopore reads using LAST can be found here - pay attention to the comments, where I've identified bits in the steps which might trip up people trying to ...
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2 votes

What is the index fastq file (sample_I*.fastq.gz) generated when demultiplexing Illumina paired-end runs?

It took me a while to figure out that the "index" is the same thing as the "barcode" that says which sample each sequence is from on a multiplexed run. If your data is not demultiplexed (single <...
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1 vote
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Get frequency of index sequences of fastq file

I actually went back to the output folder on the MiniSeq and found this file: DemultiplexSummaryF1L1, which contains demultiplexing information of the whole run. ...
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1 vote

Get frequency of index sequences of fastq file

I don't know that you can get them from that file. I've noticed that when the Miseq is left to run its version of fastq generation software, there are no indices in the undetermined file. I usually ...
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1 vote
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Demultiplexing FASTQ file without index information

I would suggest looking at sample metadata: Library: Name: TruSeq RNA Instrument: Illumina HiSeq 2000 Strategy: RNA-Seq Source: TRANSCRIPTOMIC Selection: PolyA Layout: PAIRED You can see that ...
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1 vote

cellranger mkfastq with full path to --id flag

You should be able to use the --output-dir argument to specify a folder of your choice and use --id=demux_10x as before.
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1 vote

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...
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