3 prime end enlongation

[Frederico Moraes Ferreira]

Hi devs and users, 

Has anybody happen to know if Trans-ABySS can use a RefSeq transcriptome assembly to extend the 3 prime ends of aligned sequence reads? 

I have been unsuccessfully trying to use the ESAT (End Sequence Analysis Toolkit), but it maintenance seems to  be frozen. Does anyone know an alternative program to do that?

Any clues are appreciated.

Fred

ref.:

Derr A, Yang C et al.. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Genome Res. 2016 Oct;26(10):1397-1410. 

[Ka Ming Nip]

Hello,

Trans-ABySS is a reference-free transcriptome assembler; it does not use any references at all.

You can, however, align your reads to a reference transcriptome and extract the 3'end reads for Trans-ABySS to assemble.

Alternatively, you can use RNA-Bloom (https://github.com/bcgsc/RNA-Bloom), which has a reference-guided assembly mode and an option for prioritizing the assembly of poly-A tails. This use-case has been illustrated in this preprint: https://www.biorxiv.org/content/10.1101/710699v2.full. If you installed RNA-Bloom from conda, then the command should be as simple as:

rnabloom -left reads_1.fastq -right reads_2.fastq -revcomp-right -ref reference_transcripts.fasta -polya -outdir your_output_directory

If you need help with RNA-Bloom, please create an issue here: https://github.com/bcgsc/RNA-Bloom/issues

Hope that helps!

Ka Ming

--
Ka Ming Nip, PhD
Collaborator | Dr. Inanc Birol Lab
Canada's Michael Smith Genome Sciences Centre

---

From: trans...@googlegroups.com <trans...@googlegroups.com> on behalf of Frederico Moraes Ferreira <frederico...@gmail.com>
Sent: July 20, 2023 11:21:05 AM
To: Trans-ABySS
Subject: 3 prime end enlongation

 

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[Frederico Moraes Ferreira]

Hi Ming, 

Tanks for helping. I'm gonna  give RNA-Bloom.

I'll let to know the results.

Best

Fred