-
Hi Sam, its me again here.
Tried running the program again with TCGA samples, but unfortunately immediately ran into this new error.
When running the preprocessing, I realise that the tag direc…
-
Hello. Thank you for this package. I'm doing an integration analysis using more than 40 scATAC samples. However, I do not have scRNA data from the same cells. I tried doing the label transfer using th…
-
### Description of the bug
Experiencing 137 on samtools sort, after talking with slack community and seqeria, seems to be related to [this](https://github.com/nf-core/methylseq/pull/330)
### Command…
bc2zb updated
3 weeks ago
-
Hi, run command :
singularity exec -B $PWD:$PWD braker3.sif braker.pl --useexisting --species Brachymystax_lenok1 --genome ./s3_repeats_screen/A1.genome.masked.final.fasta --prot_seq ./s1_input_da…
-
Hi RMolania! Thanks for the very useful approach. I want to use RUV-III with PRPS for non-TCGA RNA-seq data, but I don't know how to process the non-TCGA RNA-seq data to use RUV-III with PRPS. Would y…
-
Hi,
I am currently trying to run Taiji on a set of WT and KO RNAseq and ATACseq data. To not mess with previous analyses I decided to use the already existing gene quantification, which I did with …
-
Hi,
I am currently trying to apply your approach to identify potential RNA editing regulation in our own RNA-seq data, however I am having issues generating a list of editing sites.
Could you ple…
-
Hi!
First off, thank you for this analysis tool!
I am analyzing some Perturb-Seq data and have followed the vignette. I ran Mixscale_Scatterplot and interestingly the perturbation score seems p…
-
Hi, developer,
I've single-end stranded data, and specified --rna-strandness R in Hisat2 runs. So the bam alignment contain XS: tags. When running Stringtie, should I specify the --rf/--fr paramete…
-
Hi BRAKER developers,
I've been using BRAKER3 with RNA-seq data produced from VARUS, on our university HPC using singularity.
The first step of GeneMark-ET runs fine then I get an error when tra…