AnchorWave

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What information Anchorwave require to be able to parse the gff file correctly?

3

Hi, First, congratulations on the development of Anchorwave, it seems a great addition to the Comparative Genomics toolkit! I have several questions, the majority linked to the "Empty CDS file...

diaspj

example data core dumped "{EXE}_sse4.1""$@"

6

Hi, Dr Song, Thanks for your wonderful tool. I meet an error when run the example(guideline zea & sorghum). wget ftp://ftp.ensemblgenomes.org/pub/plants/release-34/fasta/zea_mays/dna/Zea_mays.AGPv4.dna.toplevel.fa.gz wget ftp://ftp.ensemblgenomes.org/pub/plants/release-34/gff3/zea_mays/Zea_mays.AGPv4.34.gff3.gz wget http://ftp.ensemblgenomes.org/pub/plants/release-54/fasta/sorghum_bicolor/dna/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.dna.toplevel.fa.gz gunzip *.gz anchorwave gff2seq -r...

HozumiLv

How should I align chromosome regions between distantly evolutionary species?

1

Hello, I am currently working on a comparative genomics project and I would like to align chromosome regions between distantly evolutionary species, specifically chicken, mouse, and human. I came across...

Rafaelsoler13

running proali from custom gff files

2

Hi, I am trying to run anchorwave as an alignment step of the buckler lab PHG pipeline. proali step is failing, and seems to me like the problem is that...

aleksicmil

AnchorWave on a very repetitive plant genome

7

Hi, I have been testing AnchorWave (v1.0.1) on a very repetitive plant genome (Faba bean, 13 Gb), but the run time has been extremely long. Alignement of a single chromosome...

agolicz

Error in MAFToGVCFPlugin

1

Hi thanks for adding the MAFToGVCFPlugin! I'm guessing something is wrong with my alignment MAF file, but I'm having a hard time narrowing down to how to fix this error....

ccmenard

Lack of understanding of MAF to VCF conversion

1

It is a bit difficult to use MAFToGVCFPlugin to convert MAF files to VCF. Is there any other way to convert MAF to VCF? I lack a certain understanding of...

Deng-Yuan

Identify Duplication

2

Hi, I have been testing Anchorwave, to check the genome duplication. It didn't give me expected result with -R 1 -Q 3. I checked MAF and converted MAF to many...

wyim-pgl

How to align the genomes at conting or scaffold level？

1

Hello, Dr Song, Thank you for developing such a powerful tool. When I use it, I find that the genomes seem to must be at the level of chromosome assembly....

naturalstay

Anchorwave large chromosome error

2

Hello, We are currently trying to run Anchorwave on the huge Axolotl genome (32 Gbp) and we are getting the following error: Command: ``` anchorwave proali -t 19 -i GCF_000001405.39_GRCh38.p13_genomic.gff...

diego-rt