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Hello,
There seems to be an error at the fastq-fasta conversion, or fastq filtering step. Can you provide advice based on the error message below? I have 180 fastq samples and it seems to proceed t…
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Dear author, I have read the article your team published in nature genetics. It's a really good study! Thank you for writing this detailed tutorial, which was very helpful for me to learn how to analy…
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Hi,
I am trying to run CRISPR-Correct with just one fastq file (R1 only). According to the readme it should be possible to do so.
How should I define the fastq_r2_fn parameter as it seems to be re…
Edert updated
20 hours ago
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**Describe the bug**
ONT scrubbed fastq subdir is `scrubbed_fastq` and Illumina's is `fastq_scrubbed`. The inconsistency causes issues downstream.
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I install atlas with conda (Atlas version 2.19)
I have 8 samples. Each pair-end sample is composed of _1.fastq and _2.fastq.
The input folder fqinput contains files:
SRR12072177.clean_1.fastq SRR1…
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### Description of feature
Hi, I couldn't run the pipeline on some smart-seq datasets which contains only single-end fastq files. I tried with two different samplesheets and get an error that fastq_2…
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### Description of the bug
Similar to #374 perhaps, I get a `Path value cannot be null` error when running `--aligner cellrangerarc`.
My sample sheet is:
```
sample,fastq_1,fastq_2,fastq_barcode,sa…
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### Ask away!
Hi @SamStudio8 @sarahjeeeze @amblina @cjw85 @nrhorner
I am running nextflow run epi2me-labs/wf-transcriptomes -r v1.2.0
with --transcriptome_source reference-guided --cdna_ki…
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Hello, I am trying to extract COI genes from raw Illumina sequences of cestodes to try and ID the hosts. I am using the cestodes as a proof of concept but would eventually like to try it with whole ge…
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Hi, thanks for producing this great software. I've a suggestion to add a check of user input.
The documentation states "The default running mode is paired-end and requires an even number of FASTQ f…