RNA-Bloom
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:hibiscus: reference-free transcriptome assembly for short and long reads
Hello! Thanks for your helpful tool! I am trying to assemble long-read sequencing data with short-read polishing. My long read data (nanopore direct RNA sequencing) are from the animals under...
This pull request addresses an open issue in Racon (https://github.com/isovic/racon/issues/233), where Racon encounters an error if reads and contigs have identical names. In our project, we have read files with...
All the files I need to run this on are in a directory. Is there a way I can give the path to the directory in -long rather than listing...
I ran rnabloom on several of my input files individually. out of my 10 samples, it did not produce any transcriptome file for 2 of them. Why is that? It...
I ran bloom on multiple fastq files together by giving it 200GB ram. It gave me out of memory exception mid way. I was running the command using a salloc...
After running Oxford nanopore direct RNA sequencing with total RNA as input, I preprocessed the data through fastp and then input the result for assembly with RNAbloom2 with the following...
# Please report - [x] version of RNA-Bloom with `java -jar RNA-Bloom.jar -version` 2.0.1 - [x] version of java with `java -version` 20 - [x] exact command used to run...
# Please report - [x] version of RNA-Bloom with `java -jar RNA-Bloom.jar -version` RNA-Bloom v2.0.1 - [x] version of java with `java -version` openjdk version "18.0.1" 2022-04-19 - [x] exact...
# Please report - [x] version of RNA-Bloom with `java -jar RNA-Bloom.jar -version` 2.0.1 - [x] version of java with `java -version` 20 - [x] exact command used to run...
It would be very helpful to have a reference-guided assembly available for the long-read functionality of rnabloom.
