Kristoffer

Great that you solved it, I will implement this fix. The new bug looks easy to solve, `mp6k75.bwa.bam` seems to be a directory (last line in error message). Remove this...

Honest answer is that I don't know yet. We are currently testing it and preliminary results show that it _can_ give significant gain in some cases, but not all. We...

Hi @Malabady, The `--consensus` parameter was an experimental parameter added after publishing isONclust. It has not been tested well and I would simply suggest not to use it in isONclust....

...and as for the actual runtime error I don't know. As you mention, if you are able to run spoa without error on the instance reported in the error message...

Hi @nextgenusfs, **Q1:** Homopolymer compression mainly helps for transcriptome data as it removes polyA tails. I'm fairly sure you can simply change one line (274) [here](https://github.com/ksahlin/isONclust/blob/master/modules/cluster.py#L274) from ``` seq_hpol_comp =...

Ah, don't know how I missed that, I was looking for the quality values too.. Sorry about that. Yes, your fix looks good from what I can see.

Hi @lauraht, You are right that it can be challenging distinguishing between structural differences and errors accumulated in regions using only the minimizes. There is no tailored way to do...

I think I know what is going on. First off, isONclust does not hande reverse complements, therefore, it will put all the forward oriented reads in one cluster and reverse...

Also, about the number of shared minimizers: it is difficult to state anything about this. You can try a denser sampling of minimizes (as proposed in the previous message). Your...

Hi @lauraht, The k and w are used to find initial candidate clusters - so yes, they matter. An alignment won't be tested between a read and representative that has...