RNA-Bloom

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RNA-Bloom Generates Empty FASTA Without Error

8

As per title. Input file: [test.fastq.gz](https://github.com/bcgsc/RNA-Bloom/files/9286125/test.fastq.gz) Command: ```bash rnabloom -t 2 -outdir test_out -long test.fastq -ntcard ``` It should probably again report too little input data? Big thanks for all...

schorlton

ERROR: For input string: "9223372036854775808"

6

Another error which seems to be from too few/too short reads as input? But pretty cryptic. Thanks again!! ```bash root@633c29844365:/data/retry# rnabloom -outdir rnabloom_out -t 8 -long filtered.fastq -ntcard RNA-Bloom v1.4.3...

schorlton

# Please report - [x] version of RNA-Bloom with `java -jar RNA-Bloom.jar -version` 2.0.0 and earlier versions - [x] version of java with `java -version` jre-11-openjdk-11.0.16.0.8-1.el7_9.x86_64 - [x] exact command...

kmnip

Transcript headers follow different formats

3

# Please report - [x] version of RNA-Bloom with `java -jar RNA-Bloom.jar -version` - [x] version of java with `java -version` - [x] exact command used to run RNA-Bloom Trying...

schorlton

Feature Request: More verbose logging?

1

# Please report - [x] version of RNA-Bloom with `java -jar RNA-Bloom.jar -version` - [x] version of java with `java -version` - [x] exact command used to run RNA-Bloom Same...

schorlton

How to restart a failed run

1

# Please report - [v1.4.3 ] version of RNA-Bloom with `java -jar RNA-Bloom.jar -version` - [ 11.0.9.1] version of java with `java -version` - [ ] exact command used to...

jesgomez

How to remove the isoform in the trasncript.fa file?

3

Hello , I am doing the denvo transcriptome assembly, please guide me how to remove the isoforms in the transcript.fa file, The output of transcript.fa file has transcript start as...

mathavanpu

Coverage does not add up

4

Thanks again for your help! When using RNA-Bloom, I expected (perhaps naively) that the sum of `coverage of each contig X length of same contig` would not exceed the number...

schorlton

ERROR: Error during redundancy reduction!

1

# Please report - [x] version of RNA-Bloom with `java -jar RNA-Bloom.jar -version` /Bio/User/software/anaconda3/envs/rnabloom/bin/rnabloom RNA-Bloom v2.0.0 - [x] version of java with `java -version` /Bio/User/software/anaconda3/envs/rnabloom/bin/java -version openjdk version "17.0.3-internal" 2022-04-19...

xiekunwhy

RAM requirements. What is the minimum?

2

Hello, I just wanted to ask what the minimum RAM requirements are for using RNA-Bloom. I am interested in performing a _de novo_ alignment of a pathogen transcriptome from previously...

nriareal