Agnieszka Golicz

Oh pggb looks very nice, I did not know about it! Unfortunately, I don't have the data yet. But I would be happy to share when it arrives (although it...

Thanks, I was afraid that may be the case. In case of hitting chromosome size limits I suppose I could split up chromosomes at the same location across assemblies. To...

Many thanks again. I am sure I will be back when the data arrives! All the best, Agnieszka

Hello, As promised I return :), now that we have some data. We have assemblies for two genomes and I tried to build a graph with pggb for one of...

Linking this to #62 as they appear to be similar issues. @egoltsman did you ever find a solution? It would be great to have information about 'what portion of the...

Sorry, one more question, does TPMCalculator support stranded libraries and if not is there a plan to add that feature? I thought it might have been included in v0.04. I...

Thanks. That's where my question comes from. I checked a couple of examples and it looked like it is 1-based, which is more gff/vcf than bed style.

Thanks! We will give it a try see how it goes.

Unfortunately I have not had the time yet. Hopefully at the beginning of next year. EDTA https://github.com/oushujun/EDTA, seems like a good candidate for plant repeat library creation.

Would it also be possible to add fasta header format (>xxx) for the TE library and the repeatmasker command to be used with that library?