Sancar Adali

build from source

1

I am trying to build these project from source. There are too many dependencies that I cannot keep track of and I don't have root privilages on this machine. While...

tombo text_output browser_files outputs succinct error

4

I am running this tombo command with detect_modifications `log = !tombo detect_modifications model_sample_compare --fast5-basedirs {sam_nanopores_seq_shape_mod_fast5_dir} --control-fast5-basedirs {sam_nanopores_fast5_dir} --rna --statistics-file-basename sam_nanopore_RNAshape_stats_rep_via_ipy --per-read-statistics-basename sam_nanopore_RNAshape_per_read_stats_rep_via_ipy --minimum-test-reads 100 --multiprocess-region-size 250` and then run `tombo...

I have run into the following problem with detect modifications mode of tombo. Normally I run the tombo commands in an jupyter notebook, but I decided to run these via...

The tombo command I run is tombo plot most_significant --fast5-basedirs ./METEORE/data/example/ --pdf-filename tombo_result_1 --statistics-filename example.CpG.tombo.stats The R runtime error is like this: RRuntimeError: Error in eval(expr, envir, enclos) : object...

So I am using a devtools build of the main branch of the pkg. I have a vector of ICD10 codes, and the output vector is shorter, to my understanding...

Tombo can generate per-read statistics for differential modification. Based on the xpore approach described in your paper, xpore should also be able to compute mixture weights for each read. Does...

For a given pdb, the native sequence extracted from the file may be a different length than the variant sequences of interest . I want to score those variant sequences...

deeplexicon produces different demultiplexing results for GPU and CPU mode.

8

For the RNA samples I am running, demultiplexing gives significantly different results. GPU mode results has a lot more unknown assignments and very small number of bc3 barcoded reads. Meanwhile...

rpy2 package which is required by tombo's plotting functions is not installed in mopmod singularity images

2

I am trying to use "tombo plot" commands to run plotting functions of ont-tombo 1.5.1 . I am getting a "rpy2 is not installed" error message , and I checked...

evaluation for image retrieval does not work. numpy array size mismatch

2

I get the the tensor size error at the end. The command I am running is this: ` python eval_retrieval.py --bert_model bert-base-uncased --from_pretrained save/RetrievalFlickr30k_bert_base_6layer_6conect-pretrained/pytorch_model_19.bin --config_file config/bert_base_6layer_6conect.json --task 3 --split test...