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Gzipped fastq files

1

Can Jellyfish read gzipped fastq files and, if not, can uncompressed fastq be piped into Jellyfish. Thanks,

Hi all, I tried to do gene prediction with Quast, but the process failed due to error. Quast was ran with the following gene prediction options: --eukaryote --gene-finding The error...

We have fast5 files generating using the RNA002 chemistry. We are interested in determining the methylation status (5mc) of these reads. How do we proceed to do this Bonito? Alternatively,...

We are trying to detect a deletion using Nanopore long read data. We think that the size of the deletion is something around 10-15 kb in size, although we are...

ref kmer and position of modification

2

If a significant change in methylation is detected, at which base pair is this change? Is it the position indicated by the pos column or perhaps the middle of the...

Direction of change in methylation

1

If a significant change in methylation is determined at a particular position, how can one determine the direction of change. In other words, is there any way to determine if...

> devtools::install_github('satijalab/seurat-data') Using GitHub PAT from the git credential store. Error: Failed to install 'unknown package' from GitHub: HTTP error 401. Bad credentials Rate limit remaining: 51/60 Rate limit reset...

Doesn't match if U nucleotide used in sequence

3

If you have an RNA sequence with U's, the U's will have to be converted to T's to get an alignment. Just something users might want to be aware of.

Collapse beta values in EPIC v2 arrays with betasCollapseToPfx

1

I am interested in combining methylation data. For example, I would like to combine cgXXXXXX_BC21 and cgXXXXXX_TC21 into a single value. There is a function in the sesame package called...

module 'tensorflow' has no attribute 'reset_default_graph'

4

I have Tensorflow installed. When I check the version, it is 2.12. tensorflow::tf_config() 2023-02-27 15:55:21.780906: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations....