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Hiya,
Can Arriba be used to detect fusions in single-cell RNAseq data (e.g. Smart-seq2). I expect to see a greater number of false positives compared to bulk RNAseq, and with a lower number of read…
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Hi,
I'm using stringtie to assemble a transcriptome using a reference annotation made with a predict annotation containing only CDS regions.
This is the command line I'm using:
```
stringtie…
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Hello,
I wanted to download Splice Junction files for the Primary Tumors of the TCGA-GBM project. I am runnin g R 4.0.0.
I used the command
`query The columns of the SJ.out.tab file have the follo…
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Hi,
Is it possible to speedup eventalign computations by splitting the files and/or region windowing?
For example to speedup `nanopolish eventalign --reads all.fastq --bam all.bam --genome geno…
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Hi there,
I recently upgraded by bcbio install (I had to use the method recommended at https://github.com/bcbio/bcbio-nextgen/issues/2676 to get around conda issues). Testing the new install, I …
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Hi,
I am trying to get STAR to work for finding fusion transcripts in PacBio (Iso-Seq) data. Previously I have been using GMAP coupled with a [downstream python script](https://github.com/PacificBios…
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Hello.. I am currently having an issue with the annotation part. I am using Linux to perform CIRCexplorer2 analysis.
After aligning everything with STAR as described by you,
for instance:
`S…
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Hi
I have a general question pertaining to quantifying QuantSeq data and comparing Salmon vs the alignment methods recommended by Lexogen (Star/Bowtie followed by htseq to get read counts per gene)…
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- [x] **Moving "scary" warning messages to the verbose option**
The following warning message pair (which addresses the same issue) is only one of hundreds of similar warning messages that occur wh…
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Hello,
Thank you for setting up this repo! I was wondering if this data has been published yet and if so what paper we can cite to use this data?
Cheers,
Richard