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### Description of feature
Following up on https://github.com/nf-core/rnaseq/pull/1369#discussion_r1744079079.
@MatthiasZepper Please take over this issue.
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### Description of the bug
```bash
nextflow run main.nf \
-ansi-log false \
-profile docker,gcp \
-work-dir gs://path/to/bucket/scrnaseq/work \
--input samples.csv \
--protocol…
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Hi, I really like your approach for modelling ordinal data and am trying it on my data. I have gene expression data and ordinal response data as well as categorical unpenalized factors. I have split m…
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Hello! I am using STAR-Fusion to generate fusion transcripts for the RNA-Seq data of _Arabidopsis thaliana_
**I have first used the Ensembl Plants 51 (latest) version of gtf file and I could not ev…
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Hi,
In the mapping with tophat-fusion step, I get the below error:
```
$ clear_quant -1 206_1.fq.gz -2 206_2.fq.gz -g /library/hg19.fa -i /library/hg19.fa -j /library/hg19.fa -G /library/hg19.g…
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Dear MAVIS team.
Hi I'm Oh.
I have two questions.
Q1. If I change reference or annotated files, can I visualize viral integrations?
Q2. I found the following fusion. (the Promoter of TP53…
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I try to do this tutorial using conda enviroment.
I have this error:
```
n.pre_blast_filter -E 0.001 --genome_lib_dir /home/centos/illumina/TEST_FUSION/STAR-Fusion-Tutorial/ctat_genome_lib_build_…
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Hello Dr. Dobin,
I am optimizing the options of STAR to detect fusion genes, and have two questions.
1. Unmapped reads in 'Chimeric.out.junction'
The unmapped reads with STAR are mapped in Chi…
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Hi @brianjohnhaas,
I used --denovo_reconstruct command but faced the following error.
`Running: /home/ubuntu/miniconda3/envs/starFusion/opt/trinity-2.8.5/util/misc/process_GMAP_alignments_gff3_c…
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I'm using the latest mfannot via docker image.
I'm annotating a fungal mt genome with [genetic code 4](https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG4), and some of the ORFs were probl…