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I installed lrgasp-tools and ran:
`lrgasp-validate-models models.gtf.gz` on one of my files. The command terminated without printing anything.
It's not very clear what the expected output is. Does a…
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Route id format is different in the original Jore data and the GTFS data set. The match the GTFS route ids, we need to drop the last character of the route id when it is a number.
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As the bbnavi OTP uses the [VBB](https://vbb.de/) both [on production](https://github.com/bbnavi/opentripplaner-berlin-brandenburg/blob/8231e157b5609a9b5230b356fc5db3a80eedde1b/Dockerfile#L11) and [on…
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`-ht` doesn't run if a GTF is not provided.
# Runs
`modbamtools plot --batch genes.bed --gtf gencode.v38.annotation.sorted.gtf.gz -ht --cluster --prefix test_batch_hp_removed_gm12878_batch --sampl…
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I tried to run isocirc with test data. It worked great! However, when I tried to run isocirc with my own data, it did not generate isocirc.out, isocirc_stats.out or isocirc.bed. I downloaded the fa d…
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Hello, I have a question in terms of the detailed GTFS data requirements.
**Describe the bug**
I want to use the function `TravelTimeMatrixComputer`, and for the `departure time` I typed in one ti…
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We will need to perform quality control on sequencing reads, `BAM` files generated by aligners and alignment statistics output by aligners.
Use the small `BAM` file provided at the following [link…
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```
The routes.txt file in GTFS has a column for route short and route long names.
The converter populates route_short_name and leaves route_long_name empty. It
might be desirable to populate long n…
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Hello,
I was trying to use PAS2GEF to create reference using the latest Ensembl GTF file but were unable to do so. I have attached a screenshot with the error messages that showed up on R. Hope you…
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Hi,
I am running stringtie merge and then gffcompare:
`gffcompare -r gencode.gtf -G -o gff stringtie_merged.gtf`
When I look at the gff.stringtie_merged.gtf.tmap all values are zero for FPKM,TPM, …