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I am trying to create a probe set for Symbiodinium but am stuck on the duplication removal step due to a memory issue. I was able to complete the run using a selection of Sgou+3.temp.probes-TO-SELF-PR…
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Aligning closely related bacterial genomes I observed frequent messages like this:
```
INFO - Finished 5. alignment (5 to go; 50.00 % done)
truncating alignment ending at (759335,706960); anchor a…
iimog updated
5 years ago
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jcvi.graphics.ribbon module is a modified version of the synteny module which allows plotting of arbitrary alignments and multiple genomic feature tracks. Ribbon plots are not based on ortholog linkag…
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Hi,
I get this kind of error every couple of screens during RunLastzChain.sh (http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto#Example.2C_step_1:_Alignments_with_Blastz) execution an…
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I was wondering if you could provide support for reading the input genomes in .fa.gz files:
```
lastz hg18.chr4.fa.gz galGal3.chr4.fa.gz --format=maf > hg18_4_vs_galGal3_4.maf
```
To my unders…
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when i run :`cactus ./js_grass ./test_grass.txt ./test_grass.hal --binariesMode singularity --batchSystem slurm --consCores 1 --maxJobs 1` ,I get errors :`root filesystem extraction failed: failed to …
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Hi
I have Cactus 2.0.5 and I am using a set of 6 primate genomes to test the speedup due to SegAlign on a GPU-enabled cluster node. I installed Cactus from binary tarball and then a separate manual…
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By default, cactus runs cigars output by `cPecanLastz` through `cPecanRealign`. This can be toggled off by setting `realign="0"` in the `` part of the config. When using the GPU lastz, the chunksize…
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Hello,
I am trying to align the genome from one cultivar to the other cultivar of green foxtail using lastz with
`lastz Sv-A10.1-Chr01.fa Me34V-scaffold1.fa --seed=match12 --notransition --coverage=…
xiuru updated
3 years ago
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## This is a practical guidance for generating the most conserved elements of drosophila simulans
- [ ] Prepare the working directory.
- [ ] Prepare the genome data.
- [ ] Set the follow…