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Gregor-Mendel-Institute / bookend

End-guided RNA assembler
MIT License
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Small size of certain samples assemblies #3

Open hacaoe opened 2 years ago

hacaoe commented 2 years ago

Hi, I am currently working on using bookend together with flair to generate transcriptomes of multiple samples and I am having a weird issue. For some samples, my bookend assemblies are way smaller than for other assemblies (around 100 KB instead of like 9 MB in other samples). What would be the reason for this, when the elrs are of similar size and no different parameters were chosen between the different samples? A quick reply would be appreciated

hacaoe commented 2 years ago

Also, is it possible to specify amount of threads for bookend, so that it could run faster?

maschon0 commented 2 years ago

Hello @hacaoe,

The difference in assembly sizes could have a variety of causes. Could you share the arguments you are using for assembly, as well as an example of an ELR file that produced a large vs. a small assembly?

It may be worthwhile to re-run ELR generation and assembly using the new major release version 1.0.1. You can see the release notes here, but I identified a number of bugs that were causing reads/assemblies to be lost, and I have corrected them in this release. You can either install from source code here or pip3 install bookend-rna --upgrade if you installed through pip.

Unfortunately multi-threading is not currently implemented, so Bookend utilities can only run on one core at the moment. This is on my to-do list to implement.