Questions tagged [demultiplexing]

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pacbio demultiplexing issue

I was wondering if there is a way to provide pacbio lima demultiplexing only a barcode, and let lima demux sample even if only one end has the barcode, not both?
cautree's user avatar
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1 vote
1 answer
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Running cellranger on scRNASeq data with feature barcoding (10x + antibody capture)

I can't seem to find a clear answer to this question, so here it goes: I have sequenced scRNASeq + scVDJSeq (TCR) data, which has been sequenced using feature barcoding from 10x genomics, via antibody ...
h3ab74's user avatar
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2 votes
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STACKS: process_radtags only reads 1 input file and returns >90% barcode not found drops

I am trying to demultiplex some paired-end ddradseq data and am running into an issue with STACKS in that the program only seems to read 1 of my files for input (there are 2) and also results in over ...
heather_l's user avatar
1 vote
1 answer
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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 ...
gc5's user avatar
  • 1,783
2 votes
0 answers
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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 ...
AlixSil's user avatar
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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 ...
divibisan's user avatar
  • 101
2 votes
2 answers
466 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 ...
justinian482's user avatar
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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 ...
Geo Vogler's user avatar
1 vote
1 answer
860 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: <...
Stewart Russell's user avatar
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2 answers
201 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 ...
BCArg's user avatar
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3 votes
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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, ...
AmadeusDrZaius's user avatar
6 votes
2 answers
3k 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 ...
Martín Terán's user avatar
3 votes
0 answers
714 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 ...
gc5's user avatar
  • 1,783
11 votes
3 answers
10k 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 ...
conchoecia's user avatar
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1 answer
235 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 ...
gc5's user avatar
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