sunta3iouxos

Hi all, Any recommendations on how to trim the generated fastq files from this library using fastP? The default options can not automatically recognize the adapters. The adapters used are...

dotplot: wrong orderBy parameter; set to default `orderBy = "x"`

2

The plot is created, but I have no idea on the error. I have a DEG set produced by DeSeq2. I get the sorted ranked with ENSEMBL names (hg38) as:...

annotatePeak : 'select()' returned 1:many mapping between keys and columns

1

Hi all, running ChiPseekeer, list> preparing features information... 2020-05-12 09:31:44 >> identifying nearest features... 2020-05-12 09:31:44 >> calculating distance from peak to TSS... 2020-05-12 09:31:46 >> assigning genomic annotation... 2020-05-12...

implement parallel multithreaded reading on Flat files to avoid splitting

1

Hi there, I am using the latest sortmerna from github and I used it with the following commands: ```` ./sortmerna --ref /projects/ccg-ngs/production/sw/sortmerna/rRNA_databases/silva-euk-28s-id98.fasta --ref /projects/ccg-ngs/production/sw/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta --ref /projects/ccg-ngs/production/sw/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta --ref /projects/ccg-ngs/production/sw/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta --ref /projects/ccg-ngs/production/sw/sortmerna/rRNA_databases/silva-arc-23s-id98.fasta...

Support analysis of spike-in sequences

4

Hi all, Does this pipeline handles spike ins (like the PhiX from illumina)? thank you in advance

Thank you for this extension. The following is a feature request and probable a question of function that I might not be aware. Before some updates, I could keep track...

dotplot() error after compareCluster() for fun = "groupGO" with data(gcSample)

1

### Describe your issue Even using the example from the documentation I am getting errors: ```R > xx clusterProfiler::dotplot(xx) > xx clusterProfiler::dotplot(xx) Error in `geom_point()`: ! Problem while computing aesthetics....

Allocation of 40.69 GB for suffix_array failed.

4

I am running bwa-mem2 locally, and I got the following error bwa-mem2-2.2.1_x64-linux/bwa-mem2 index /GRCm38_gencode19/genome.fa Looking to launch executable "bwa-mem2-2.2.1_x64-linux/bwa-mem2.avx2", simd = .avx2 Launching executable "bwa-mem2-2.2.1_x64-linux/bwa-mem2.avx2" [bwa_index] Pack FASTA... 15.66 sec...

spikeIn sampe scaling factor calculation discrepenses

2

I am getting different results using the multiBamSummary command on my local PC using the following command that I expected to be the same on the server side, and I...

no spikeIn chromosomes found with extention _spikein

12

Hi Katarzyna and everyone else, I can not run the spikeIns strings for Chip-seq, this is a CUT&RUN protocol that has the bacteria cary over that can be used to...