Mustafa Elshani

Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:RNA_FUSIONS_JAFFAL:UNTAR (null)'

1

I have been getting this error ``` Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:RNA_FUSIONS_JAFFAL:UNTAR (null)' Caused by: Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null) Tip: when you have fixed the problem...

Unknown process directive: `validExitStatus`

2

This seems to be an issue logs are here ` Check script '/root/.nextflow/assets/likelet/LncPipe/LncRNAanalysisPipe.nf' at line: 1038 or see '.nextflow.log' file for more details` logs are here ``` Sep-20 14:17:05.816 [Actor...

These are SUP results from RTX8000 `gpu,gpu_memory,gpu_memory_used,gpu_driver_version,cuda_version,guppy_version,guppy_model,chunk_size,chunks_per_runner,num_basecallers,runners_per_device,samples_per_second Quadro RTX 8000,8192,76.63484928000000000000,520.61.05,11.8,6.0.6+8a98bbc,sup,2000,1024,4,12,3.97501e+06 Quadro RTX 8000,8192,40.96000000000000000000,520.61.05,11.8,6.0.6+8a98bbc,sup,2000,1536,4,12, Quadro RTX 8000,8192,95.25575680000000000000,520.61.05,11.8,6.0.6+8a98bbc,sup,2000,160,4,12,2.80052e+06 Quadro RTX 8000,8192,97.77561600000000000000,520.61.05,11.8,6.0.6+8a98bbc,sup,2000,256,4,12,4.0642e+06 Quadro RTX 8000,8192,101.03439360000000000000,520.61.05,11.8,6.0.6+8a98bbc,sup,2**000,512,4,12,4.15801e+06** Quadro RTX 8000,8192,107.52000000000000000000,520.61.05,11.8,6.0.6+8a98bbc,sup,2000,786,4,12,3.92427e+06 `

HGNC or Gene symbol

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Currently frustrated when count matrix only has ENSG id, be it from ensemble or gencode Is it possible for automation of ENSG conversion to HGNC symbol Currently using biomart to...

Running tailfindr on multinode HPC

5

Hi A quick question I would like to ask if tailfindr can be run on multi-node HPC cluster, I briefly had a go and it seems that it only used...

Refining transcript 3' and 5' ends with LAPA

3

Hi @MuhammedHasan I see that you have 'lapa.correction.Transcript' how would I be able to use it. To my understanding default LAPA deals with 'gene_id' how would I change the analysis...

It seems that `lapa_correct_talon` is looking for a column named ` samples ` in the TALON generates `read_annot` file. This column is not available, however sample names are in `dataset`...

Order by polya tail length

3

Hi Great work with trackplot I currently plotted some reads which have polyA tail length as attached is there a way to order these reads by either transcript ie same...

Higher resolution .tif images for SpatialDimPlot

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I am currently working with Visium V1 data, and the Space Ranger spatial output includes a "hires" image. However, since I am working with very small tissue samples, the "hires"...

lr-kallisto dorado unaligned bam files

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Hi It is great to hear the support for long-reads coming to kallisto I would like to introduce it to our pipelines I have few question regarding running lr-kallisto on...