9
votes
Accepted
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 ...
- 3,181
5
votes
Accepted
Demultiplex nanopore reads with custom barcodes
I've written some Perl code for demultiplexing nanopore reads using LAST. A workflow demonstrating the use of this script (and how it works under the hood) can be found here:
https://dx.doi.org/10....
- 15k
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 ...
2
votes
cellranger-arc throws an error when demultiplexing
I have found the solution to my problem. The only thing missing from the command I used was the instruction to regard the run as a ATAC/GEX step. This is done by adding the parameter ...
- 223
2
votes
Running cellranger on scRNASeq data with feature barcoding (10x + antibody capture)
Check your FASTQ headers - if they've been demultiplexed, the index barcodes can be found in the header. The barcodes are usually separated by a + in the comment ...
- 2,464
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 <...
- 121
1
vote
MULTI-Seq snRNA-seq results thousands sample barcodes while there should be only 9
You don't give much information. However, here is how 10x hashing usually goes:
First, there is the per-cell barcode that tells you which gene expression reads come from one cell. CellRanger and other ...
- 1,510
1
vote
Accepted
Definition of genotype in demuxlet
The genotypes $\{0,1,2\}$ are mappings to the genotypes AA (homref), AB (heterozygous), BB (homalt) (from supplementary resources). This is also mapped to the number of alterations (e.g., 0 -> 0 ...
- 1,813
1
vote
Accepted
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. ...
- 345
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 ...
- 1,971
1
vote
Accepted
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 ...
- 4,212
1
vote
Accepted
Error processing run file with bcl2fastq - Unable to open '.../RunInfo.xml' file for reading
I repro the error.
ls /ml
ls: cannot access '/ml': No such file or directory
If run
...
M__♦
- 12.8k
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.
- 4,202
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...
- 111
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