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:hibiscus: reference-free transcriptome assembly for short and long reads
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Illumina PE (Stranded) and PacBio Reads for RNA-Seq #5

Closed sum732 closed 4 years ago

sum732 commented 4 years ago

Hello, While looking for a hybrid assembler came across RNABloom. I test rnaSpades and was not happy with the assembly. I read about RNABloom and its mentioned that ONT reads can be used. I am wondering if RNABloom is tested with PacBio reads and can I use it as hybrid assembler (illumnina +PacBio for transcriptome assembly). Thanks, Deep

kmnip commented 4 years ago

Hi @sum732 ,

Thanks for your interest in using RNA-Bloom! Hybrid assembly is currently an experimental feature in RNA-Bloom.

To run in hybrid mode, you just have to list your Illumina PE reads for -left and -right and your long reads for -long. Here is an example for non-stranded long reads:

java -jar RNA-Bloom.jar -left ${illumina_left.fastq} -right ${illumina_right.fastq} -long ${long.fastq} -ntcard -t ${threads} -outdir ${outdir}

Are your PacBio Reads stranded? If so, are they in the same orientation as the transcript? or reverse-complemented?

sum732 commented 4 years ago

Thanks for promptly responding. I was just not sure is -long with with PacBio reads ( there are examples that show ONT, so i thought that its optimized for ONT and not PacBio). The PacBio reads are unstranded.

kmnip commented 4 years ago

You can try it for PacBio. It's just the settings for mapping are not optimized for PacBio reads. I will add an option for that in the next release.

Since the PacBio reads are unstranded, you can run in non-stranded mode, as shown previously.

sum732 commented 4 years ago

Great, thanks, I will try that. I am facing an issue with the racon, perhaps you can help. Will create a new thread