Questions tagged [demultiplexing]

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Definition of genotype in demuxlet

I am reading the Online methods of the demuxlet paper. The genotype $g$ is taken from the set $\{0, 1, 2\}$, defined as "the true genotype of the sample corresponding to $c$-th droplet at $v$-th ...
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2 votes
0 answers
21 views

snRNA-seq Demultiplexing before or after QC

I'm currently analyzing snRNA-seq data and have to demultiplex them using HTODemux in Seurat. The question is : should I do my QC filters on my droplets before or after the demultiplexing ? From what ...
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0 votes
0 answers
79 views

Why is bcl2fastq2 taking so long to calculate stats?

Our lab has been using bcl2fastq v2.20.0.422 to demultiplex RNA-seq data sequenced on an Illumina Novaseq machine on a beefy EC2 instance and we've run into the strange problem: namely that while ...
  • 101
2 votes
2 answers
177 views

Get frequency of index sequences of fastq file

I recently did some sequencing on a MiniSeq and unexpectedly the Undetermined_S0_L001_R1_001.fastq.gz file contained quite a lot of data (about 40% of total). I ...
0 votes
1 answer
152 views

Demultiplexing FASTQ file without index information

I am trying to understand how data that was uploaded to SRA (https://www.ncbi.nlm.nih.gov/sra?LinkName=biosample_sra&from_uid=4510743) can be analyzed with the assumption that the FASTQ file ...
1 vote
1 answer
571 views

Error processing run file with bcl2fastq - Unable to open '.../RunInfo.xml' file for reading

I'm attempting to demux a nextseq run which I've successfully done several times in the past on other runs. I uploaded the run from my PC to the server (Ubuntu 18.04.4 LTS) without issue. Then I ran: <...
0 votes
2 answers
134 views

cellranger mkfastq with full path to --id flag

I have always used cellranger mkfastq to demultiplex 10x genomics runs manually, though recently the commands to do so have been incorporated into a script that ...
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3 votes
2 answers
1k views

How to demultiplex a mix of single-indexed and dual-indexed samples

The problem If I have a sample sheet that contains both single-indexed and dual-indexed samples, I can split it up into two sample sheets and then run bcl2fastq on each one. However, when doing this, ...
4 votes
2 answers
2k views

Demultiplex nanopore reads with custom barcodes

We have a problem trying to demultiplex MinION sequences with custom barcodes. Do you have any software recommendations we can try for demultiplexing or how to demultiplex these custom barcodes with ...
3 votes
0 answers
588 views

Fastest way to demultiplex bam file based on field

I have a bam file with aligned reads from multiple experiments. For each experiment I have a portion of the sequence identifier, thus for example ...
  • 1,773
10 votes
3 answers
8k views

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

What is the index fastq file that comes with some Illumina sequencing datasets? (The samplename_I*.fastq.gz file.) For example, I recently received some 10X ...
  • 3,101
0 votes
1 answer
219 views

Demultiplexing and preprocessing for custom single-nucleus Drop-seq data

I am trying to reproduce the preprocessing of paired-end sequencing reads in Lake et al. (ref. 1). First, paired-end reads were filtered out if read 1 had more than four non-T bases in the last ten ...
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