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==== NAME=rna.align, STATUS=RetryableFailure, PARENT=
SHARD_IDX=0, RC=255, JOB_ID=10962
START=2024-10-31T07:37:19.909Z, END=2024-10-31T07:39:09.152Z
STDOUT=/xxx/223d2898-d815-4640-a4b1-24f863fe84b3…
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I am using singularity to run this pipeline.
Unable to download requested sequence data from Ensembl (ftp://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.…
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I'm wondering if there is concise documentation somewhere for reproducing the exact analysis of the TCGA/GTEX data in this [paper](https://www.nature.com/articles/nbt.3772) (but with new samples).
h…
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Hi Håkon,
I work in Anders Lund's lab at BRIC in Copenhagen.
I’m trying to use your ORFik pipeline, mainly to do QC on a recent RIbo-seq experiment performed on mouse organoids.
But maybe also fr…
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Hello!
I now have RNA-seq data and full-length transcriptome data from several tissues, and I used "Trinity genome-guieded" to get the transcript "Trinity-GG.fasta" of the RNA-seq . At the same time,…
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Hi Brian,
I have a couple of bioinfo tools that I "ported" to modal (blat, STAR, https://github.com/tdsone/modal-rna-seq-pipeline). Do you think this would be useful in biomodals as well (biomodal…
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Hi, thank you so much for the great tool.
I'm trying to apply longshot on long-read RNA-seq data (Iso-seq data from PacBio HiFi reads).
I ran the pipeline with default options and got ~30% reads …
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# [BI] RNA-seq data processing using nf-core pipeline | Keun Hong
Link: nf-core rnaseq pipeline
[https://keun-hong.github.io/bioinformatics/rna-seq-nf-core/](https://keun-hong.github.io/bioinformati…
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See https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update for full description of each task (requires gitlab login)
- assembly accession number: GCF_040414725.1
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### Is your feature request related to a problem?
Is there a way to do differential expression of transcripts (e.g. similar to DEseq2 but for transcripts) with RNAlysis?
### Describe the solution yo…