Ka Ming Nip
Ka Ming Nip
Yes, it is just that simple! For example: ``` ABYSS_PATH=/path/to/my/abyss/bin/directory/ export PATH=${ABYSS_PATH}:${PATH} transabyss -k 32 --se read_1.fq read_2.fq ... ``` On Wed, Oct 3, 2018 at 11:09 AM Shaun Jackman...
Can you please report the exact command that you use and your entire log file? On Fri, Oct 5, 2018 at 7:39 AM kokyriakidis wrote: > Hi, after running transabyss...
@kokyriakidis Thank you. I see what the problem is now! You were using Trans-ABySS version **1.5.5** with ABySS version is **2.1.1**, but Trans-ABySS 1.5.x does not support ABySS 2.x.x. To...
Please confirm whether you have the correct version of ABySS installed. As mentioned in our [README](https://github.com/bcgsc/transabyss), Trans-ABySS only works with ABySS version 2.0.x, e.g. https://github.com/bcgsc/abyss/releases/tag/2.0.3 If you installed Trans-ABySS and...
Yes, I agree with @vlad0x00. Please install Trans-ABySS into a dedicated conda environment, e.g. ``` conda create -n transabyss -c bioconda transabyss ``` Activate this environment and try your assembly...
>Initially, I attempted to create a comprehensive assembly by merging the information from all 32 samples using the "(B) assemble multi-sample RNA-seq data with pooled assembly mode" feature. It did...
Some settings can be changed to reduce the redundancy of the assembly, e.g. ``` -indel 100 -tip 100 -p 0.6 ``` The default for these for long reads are `-indel...
Hi @elissasoroj , If I remember correctly, ABySS (without Bloom filter deBruijn graph) can only read multiple read files at the same time if it was using MPI. Trans-ABySS doesn't...
I tried the Bloom filter DBG approach in ABySS a long time ago, but it produced a worse transcriptome assembly at the time. I decided to stick with the original...
Depends on what you want to do with the transcripts? To assemble multi-sample data, you can follow the instructions here: https://github.com/bcgsc/RNA-Bloom?tab=readme-ov-file#b-assemble-multi-sample-rna-seq-data-with-pooled-assembly-mode If you don't really care about the tissue specificity...