Prakki Rama

Hi @GuangchuangYu , Thank you for creating a wonderful package ggtree. After 3 years, I also have the same question as @ghost. I have created a heatmap using gheatmap and...

Thanks so much for quick reply @tseemann. I understand the problem now. For the time being, I got rid off MN657242 plasmid from the gbk database and ran prokka without...

@tseemann noted. Thank you!

Hi Vipin, Please find it here: ``` ##gff-version 3 #!gff-spec-version 1.21 #!processor NCBI annotwriter #!genome-build ASM185804v2 #!genome-build-accession NCBI_Assembly:GCF_001858045.1 #!annotation-date 5 December 2016 #!annotation-source NCBI Oreochromis niloticus Annotation Release 103 ##sequence-region...

Hi Vipin, Thank you for quick replies. I have got the gff3 file from NCBI. The following is the result when I used the latest version of your script: ```...

Hi Vipin, Here is the annotation file: `ftp://ftp.ncbi.nlm.nih.gov/genomes/Oreochromis_niloticus/GFF/ref_ASM185804v2_top_level.gff3.gz`

Hi @vipints That appears true. Some transcripts are missing the status. Any other possible solution to think. May be I will try to approach the NCBI annotation team about this....

I had some issue with `io.BytesIO()` from the fix proposed above. So, I used `R` to generate scatter plots as below: ```py import anndata2ri import logging import rpy2.rinterface_lib.callbacks as rcb...

Hi, I ran into same problem with this today, for some strange reason, brig.jar could not detect the `blastn` from /user/path/ncbi-blast-2.9.0+/bin and kept on getting error. It resolved only after...

@jerrydodo1 You can try putting the legacy binary files of `blastall` and `formatdb` in your downloaded `ncbi-blast-2.9.0+/bin ` folder and set that as a path in BRIG.jar. Check if that...