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### Description of feature
Future plans for demultiplex workflow:
Attempt to convert into atomic subworkflows:
1. wrap different demux strategies into subworkflows:
- demultiplex_illumina (`bcl-…
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Hello,
I'm trying to run NanoCLUST with my 16S sequence data. I run it on a Linux CentOS 7 machine.
Also with the test data I get an error reaching the 'consensus_classification' module:
When I u…
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Need to convert the `Demultiplex_Stats.htm` table output by `bcl2fastq` to one or more .csv formatted tables for easier usage and importing elsewhere.
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I have looked extensively for a tool that allows parsing a sam read name to extract information and place it in a (customizable) tag, especially for UMI sequences present in read names. E.g. bcl2fast…
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Please can you specify how to use the dedup parameter WITH UMIs to dedup using the UMI information?
Also, am I able to use fastp --umi if the UMI is in a seperate file (as with Illumina bcl2fastq c…
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Hi,
I tried to install your wrapper through conda (https://anaconda.org/bioconda/bcl2fastq-nextseq) to use it in a snakemake pipeline but it fails, as it apparently requires python 2.7 :
`Specificat…
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I use fastp to process UMI per_read, as follows:
@A00153:435:HNGTVDSXX:1:1101:3712:1000:**GCTGTCA_GTCCTCT** 1:N:0:GAATTCGT+TTATGAGT
But I use Illumina bcl2fastq to process UMI ,as follows:
@A0015…
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nextseq app (to demultiplex)
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* [x] disable one-by-one entry
* [x] radio input for PE/SE and Experiments type:
* [x] runinfo model
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Good morning.
I am writing this issue because I was trying to implement CheckQC on an preliminary analysis in our company. I experienced that the tool is breaking when trying to find "percent_phix"…
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Dear all,
I've been trying to use `fgbio CorrectUmis` to process some data from Illumina's TSO500, but they use a mixture of 6bp and 7bp UMIs.
Since `bcl2fastq` needs a fixed length UMI, we've…