Ka Ming Nip

Thanks, I got your email and I was able to replicate the same issue. I created an issue for this in ntCard: https://github.com/bcgsc/ntCard/issues/73

Hi Jessica, You can simply re-run the exact same command and it should restart at stage 3. Ka Ming

Hi @schorlton, One of our collaborators reported the same issue (not on Github) when testing RNA-Bloom with just 5 reads. This error arose because the default min read depth `-lrrd`...

The transcripts in `transcripts.fa` are assembled based on extensions of seed fragments, which were reconstructed during the 2nd stage of the assembly. These fragments were split into different coverage strata....

I recommend using EvidentialGene: http://arthropods.eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html Also, refer to their preprint here: https://www.biorxiv.org/content/10.1101/829184v1.full

Thanks Kun for reporting this! In this case, you can use `transcripts.fa` (instead of `transcripts.nr.fa`) as your assembly.

The input argument cannot be a directory. If you have too many read files, then you can aggregate all the read file paths one on each line within a text...

If RNA-Bloom is a step in your Snakemake workflow, then you can run RNA-Bloom as a `shell` command within a rule. FYI: https://snakemake.readthedocs.io/en/v3.12.0/snakefiles/rules.html

There is no inference about genes. `path` indicates that it was assembled from the list of sequences from the previous step of the assembly. `s` indicates that it originate from...

You can possibly try this: http://arthropods.eugenes.org/EvidentialGene/other/sra2genes_testdrive/sra2genes4v_testdrive/ If you are interested in a crude gene groupings of assembled transcripts, I can make it a feature request (but very low priority).