Comments (4)
If you want to run the same command line, you may have to roll back to the same cactus version. Otherwise, the interface has changed a bit since then. See cactus-preprocess --help
--maskMode MASKMODE Masking mode, one of {"lastz", "brnn", "red", "none",
"config"}. Default="config".
--maskAction MASKACTION
Masking action, one of {"softmask", "hardmask",
"clip"}. Default="softmask"
Note that dna-brnn
is no longer a part of the pipeline by default, which is now usually run with a single invocation of cactus-pangenome
.
from cactus.
If you want to run the same command line, you may have to roll back to the same cactus version. Otherwise, the interface has changed a bit since then. See
cactus-preprocess --help
--maskMode MASKMODE Masking mode, one of {"lastz", "brnn", "red", "none", "config"}. Default="config". --maskAction MASKACTION Masking action, one of {"softmask", "hardmask", "clip"}. Default="softmask"
Note that
dna-brnn
is no longer a part of the pipeline by default, which is now usually run with a single invocation ofcactus-pangenome
.
Thank you so much for your reply! Sorry for the clarification, I didn't fully understand the last sentence, does dna-brnn automatically work when running cactus-pangenome or do I still have to pre-process the data with maskAction? @glennhickey
from cactus.
No, you do not need to use dna-brnn.
from cactus.
No, you do not need to use dna-brnn.
Thank you so much!
from cactus.
Related Issues (20)
- maybe the "path" do not exist in the gfa ?
- Large variation in run time and data recovery of cactus-hal2maf when switching reference genomes HOT 1
- Cactus-pangenome fails at make_vcf step only on real data HOT 3
- create phylogenetic tree with the alignment maf format HOT 7
- Multiple fasta input, single sample in vcf HOT 2
- Long Running Time and High Memory Consumption for `paffy` in `cactus-blast` HOT 8
- hal2fasta coordinates not matching with input HOT 1
- run on the grid_engine cluster HOT 1
- I want to know how cactus-pangenome adds tree file relationships. HOT 1
- MC process evolution tree file problem HOT 2
- Can this graph coverage be considered normal or good? HOT 2
- How compare mapping performance using vg-giraffe between pangenome and genomes used in pangenome construction HOT 1
- The sentence below, should`cactus-graphmap-join`be`cactus-pangenome`?
- Help parameterizing seqfile HOT 1
- Obtain node PAV, ID and fasta.
- unrecognized arguments: --bigChain HOT 1
- error cactus-align HOT 1
- How to obtain the evolutionary order of root during merge hal file HOT 1
- Preprocessing pangenome
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