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Build genome database for your own genome and #414
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Hi there, The error message says Your tsv file looks fine; maybe try using absolute paths (so replace ~ with the full path), and double check if all the files are where they are? |
I used absolute paths to run it but it still does not work. The error is with Bowtie2:
But I am putting corretly the fastq files:
|
I tried to align the samples using Bowtie2 from my PC, and actually it works
What could be happening? |
Interesting. As I am not a developer I don't think I can help beyond this. There must be something else wrong either during the building of the custom genome, or your installation. Have you tried running a test sample using the default human genome? You should consider trying that first to rule out bad installation. |
Yes! Actually the tutorial run without a problem! |
Sorry for late response, You don't those files tss file, reg2map.. They are extra data for some additional analyses in the pipeline.
How did u run Caper? It looks like it ran inside a docker container. What is the exact command line used for running Caper? e.g. `caper run atac.wdl -i input.json --docker"? |
Hello, Can you share the instructions of how to build a genome for the non-model organism? I run into so many erros. Thanks in adavance. Mary |
Hello,
I am trying to run the pipeline for chicken samples and have tried to create a custom genome reference for the pipeline. However, after finishing the steps here [https://github.com/ENCODE-described DCC/atac-seq-pipeline/blob/master/docs/build_genome_database.md] (build_genome_database.md), the tsv file I get it fails to create the tss file, reg2map... Are these files needed to run the pipeline? If so, what can I do to get them (it doesn't say anything here [https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/docs/build_genome_database.md])
Also, I am trying to run the pipeline with the json file generated, and it gives me this errors in the alignment:
This is the json file:
And this one the tsv file.
Best,
Rafael
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