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Hi,
Thanks for the nice tool!
I've been looking into using FLAMES for my gene/transcript quantification. I already have a customized pipeline for the demultiplexing/umi identification so I was l…
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### Description of feature
I know Ampliseq already uses fastqc, but I like using Seqkit stats when demultiplexing to track the number of reads that did and didn't get assigned to samples. There is an…
a4000 updated
12 months ago
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### Description of the bug
JAFFAL pipeline crashes when singularity is used because singularity container has not minimap2 (at least)
### Command used and terminal output
```console
nextflow run nf…
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Hello,
I am doing single nuclei RNA seq and have issues with cellranger discarding lots of reads and would like to directly compare between optimizing the cellranger reference to deal with overlaps e…
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Hi, Thanks for this fantastic tool!
I have been testing this tool on our pipelines and got into trouble when trying to demultiplex the 3' barcode on the second read pair.
The 5' demultiplexing w…
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**Is your feature request related to a problem? Please describe.**
Projects with many samples can produce a large amount of data in one measurement.
To analyse effects only observed in a subset of…
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Hi!
Raw Illumina reads sometimes come with the Index read as a separate file, so you get three files like that:
S0_L001_I1_001.fastq.gz
S0_L001_R1_001.fastq.gz
S0_L001_R2_001.fastq.gz
Where S…
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Hi there
Loving this --revcomp function!
I was wondering if it is possible to be selective in which of the reads to keep, i.e., reads identified with adapters in the 5'-3' or reads identified as…
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1. In the email from Genewiz after the demultiplexing they stated that the barcodes for HC5_11 and NF5_2 in Library 4 (lane 0457) were the same and therefore combined the reads into HC5_11, however on…
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Dear Xi,
many many thanks for this brilliant resource! I had one question: on https://teichlab.github.io/scg_lib_structs/methods_html/Illumina.html, the 'Truseq Read1' sequences under 'Truseq Sing…