-
Hi all,
I'm running a new installation of bcbio for the small RNA pipeline. I think it's somewhat close to the end and I get the following error. The last part of the log files is included below a…
-
I am trying to run the small RNA-Seq pipeline with paired end reads. The adapters are removed from the first reads file and the appropriate cleaned and trimmed files are generated. However, as far a…
-
Hello,
I'm a new user of bcbio and am running into errors with the small RNA-seq pipeline. I would appreciate some assistance in debugging.
I'm using the O2 cluster and the `bcbio/latest` module…
-
Hi,
First of all thanks a lot for your help and this is kinda continuation of thread #2335 . After the update I started running the code but something still confuses me just for clarification this …
-
Below is content of my configuration.
```
details:
- algorithm:
adapters:
- TGGAATTCTCGGGTGCCAAGGC
aligner: star
species: mmu
analysis: smallRNA-seq
description: PK 1
files:
-…
hmkim updated
5 years ago
-
Hi,
This is somewhat similar to #2070. We have sing end .fastq files with the following format:
@NB500965:105:HC5J5BGX2:1:11108:16467:3587 1:N:0:**ATCACG**
TTCAAGTAATCCAGGATAGG**AACTGTAGGCACCAT…
-
Hi
I'm trying to run the bcbio smallrnaseq pipeline with mirge and seqbuster but run into the following error running the dev version
```
[2018-04-25T17:01Z] ['gff', '--sps', 'hsa', '--hairpin',…
-
Hi,
Do you expect that the microRNAseq analysis capability provided by bcbio would make sense for analysis of microRNAseq data of non model organisms?
I am trying to see if I can process the Ca…
-
Hi @lpantano ,
I am using bcbio-nextgen small RNA pipeline to analyze miRNA sequencing data. The whole process executed correctly after upgrading to latest development version of bcbio-nextgen. The…
jxshi updated
5 years ago
-
Hi there,
we're trying to install bcbio with the below command:
python bcbio_nextgen_install.py /shared/pipeline-user/bcbio --tooldir=/shared/pipeline-user/tools/local --genomes hg38 --aligners bw…