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When searching for fusion genes using Arriba with a custom GTF file that extracts only the representative Ensembl ID transcripts, a large number of false positives (mostly transcripts fused at interge…
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When I run this on a small bed file I get the following error:
> [Task submitter] ERROR nextflow.processor.TaskProcessor - Error executing process > 'EXTRACT_GTF_TRANSCRIPTS'
>
> Caused by:
> …
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Hey @osm-ToniE,
We have a GTFS collection that covers all public transports in Sweden, from their [about me](https://www.trafiklab.se/about/)
> Trafiklab is a service developed and managed by Sa…
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* GitLab repo with GTFS feeds: https://gitlab.com/digitaltransport/data/africa/addis-ababa/-/tree/master/Addis%20Ababa%20GTFS_2023?ref_type=heads
* Feed in Transitland: https://www.transit.land/feeds…
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Hello,
I would like to run factR2 on a custom assembly where I ran in the issue described in [https://github.com/f-hamidlab/factR2/issues/7](issue#7). So I thought I try it on the example data you …
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Hello,All
i am trying to use Plant-LncRNA-pipline to identify lncRNAs in plants. But when i run (grep -Fwf final_lncRNA_results.txt candidate_transcript.gtf > lncRNA.gtf) this command, there is no r…
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Dear All,
I encountered an error while running whippet-index.jl. The error appears to be due to my GTF file not being in the 2.2 format. Could you please let me know where to download the correct G…
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### Description of the bug
Hello,
I recently encountered an error while running CIRIquant when providing a specific GTF file. Other tools, such as circRNA_finder, run without any issues and perfor…
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Dans datagouv le dataset [Tudbus ](https://www.data.gouv.fr/fr/datasets/tudbus-douarnenez-communaute-transport/)contient bien le GTFS (avec dans la description Fichier GTFS) et le Netex mais sur le PA…
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* Swiss NeTEX --> EPIP https://opentransportdata.swiss/de/dataset/timetablenetex_2024
* funiculars and the like NeTEx -->EPIP: https://opentransportdata.swiss/de/dataset/seilbahnen-netex
* DB GTFS…