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Greetings. Sorry this is turning into a headache.
I'm trying to install bcbio on a linux cluster. I'm having trouble getting the install working. After some messing around (I didn't realize at f…
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I used bowtie 1.3.0 for generate small RNA-seq aligments to reference genome. I used this parameters:
`bowtie -n 1 -l 10 -m 100 -k 1 --best --strata -p 24 -f /HDD/lculinaris/smallRNA/clean_data/LC01.…
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Hello everyone and especially @lpantano !
One of the bcbio users on O2 hit and an error with bcbio template:
```
upload:
dir: ../final
details:
- analysis: smallRNA-seq
algorithm:
…
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**When I ran Process with pbmc_1k_v3_fastqs data, it has follwing ERROR. And I looked up log in ouput, I did not find any other ERROR . So I thought it was something wrong with Doublets Remove, then I…
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Hi,
I would like to ask about some miRNA counts discrepancies I noticed when switching between different isomiRs versions. In past, I used isomiRs 1.10 and now I switched to isomiRs 1.16.2. I am fu…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/Mercedeh66/mirTarRnaSeq
Confirm the following by …
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Hi @lpantano
I'm trying to understand a little better how the bcbio-nextgen smallRNA pipeline deals with multi-mapping sequences. I have a dataset of 96 samples, smallRNA-seq (QIAGEN), processed t…
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Hi everyone,
I want to analyze the data of this study:
```
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68246
```
Which contains transcriptome profiling of miRNAs in 2 different cell t…
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This is partially based on the [suggestion](https://github.com/bcbio/bcbio-nextgen/issues/3100#issuecomment-591493863) by @naumenko-sa. The main idea is to organize documentation around goals and work…
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Hi,
running
`bcbio_nextgen.py upgrade --genomes BDGP6 --datatarget smallrna`
results to the
`List of genomes to get (from the config file at '{'genomes': [{'dbkey': 'BDGP6', 'name': 'D melangogast…