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Hello! I installed bcbio and have upgraded with bcbio_nextgen.py upgrade --genomes hg19. Running through the small RNA example pipeline, I am getting an error at the miRDeep2 step:
```
#Starting m…
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Hello,
I "successfully" ran the smallRNA-seq pipeline on my microRNA data and am now going through the report generation R script to check for quality and such.
I am seeing a few issues and was w…
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Hi,
We're having a problem with multiqc when using hg38 (with hg19 it seems to work).
Any ideas?
Here is an output from bcbio-nextgen:
```
`[2016-09-30T13:21Z] Run multiqc
[2016-09-30T13:21Z] [INF…
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Hello,
I am trying to run the smallRNA-seq pipeline and have created the attached yaml file for the sample and execute it as:
```
bcbio_nextgen.py ../config/bcbio.mirna.test.yaml
```
I…
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Hi again,
sorry to bother you but this feedback might be interesting - if not pls ignore.
We have used bowtie2 for alignment which does not (or maybe back then did not ) write and NH multimapper tag…
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Hello,
I am trying the new smallRNA seq analysis pipeline of bcbio.
My understanding is that it does run seqcluster and I do get a folder with this nam in work. But from the documentation I was expec…
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I'm testing the example pipeline in bcbio (small rna seq)
When I checking the data in pipeline, I saw the error log.
mirqc_bcbio/work/mirdeep2$ less error_res.log
RNAfold: invalid option -- n
sh: 1…
hmkim updated
8 years ago
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Hello,
My understanding was that there should be a mapping to known tRNA using tdrmapper (http://bcbio-nextgen.readthedocs.org/en/latest/contents/pipelines.html#smallrna-seq) and that there should be…
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Dear colleagues,
I set up A.thaliana for small rna analysis:
bcbio_nextgen.py upgrade --genomes TAIR10 --datatarget smallrna
and I saw no mirbase in the bcbio/genomes/Athaliana/TAIR10
When I run th…
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```
$ bcbio_nextgen.py ../config/Project_ID.yaml -n 16
[2016-05-22T13:05Z] System YAML configuration: /BiO/BioTools/bcbio/data/galaxy/bcbio_system.yaml
[2016-05-22T13:05Z] Resource requests: cutadapt,…
hmkim updated
8 years ago