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Note: this is my open planning doc for this project. Any feedback/suggestions welcome!
cc @freeman-lab @mckinsel @olgabot
# Overall goals
Use tabula muris data and experiences to help understand …
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Dear team,
I'm a little bit confused about the build index step. The manual says that it builds a transcriptome index but needs as input a genomic fasta and a gff. I would like to create the count…
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I found the color key range is always from -2 to 4. However, the copy number range of my data is from -1 to 2. How can I customize the range of color key? Many thanks in advance!
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Hi,
I am trying to use PlantClusterFinder. I am working on plant genome and wanted to use this tool to search gene clusters of my interest.
Therefore, I downloaded the lattest release of Plant…
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I have several done files (in alphabetical order: fastqs, remapping, retagging, variants, and vartrix) so think I'm stuck at the clustering stage (also as clusters_tmp.tsv is 0 bytes)
```
the web …
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Using the app itself as an interface should be self-explanatory. What is not self-explanatory is what the biological meaning behind all of the app's functionality is. @ajlee21 Suggested a while ago th…
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Hi developers :)
running
```
wfmash \
scerevisiae8.fasta.gz \
scerevisiae8.fasta.gz \
\
--threads 4 \
\
-n 7 -s 5000 -p 90.0 -X -l 25000 -k 19 -H 0.001 -2 30…
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I ran Trinity with a reduced dataset of only 1 time point and 3 tissues (because I had an upcoming conference) and the data I received was great. I reran Trinity with all my timepoints and tissues and…
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Thanks so much for your work in this tool and for this in advance - you guys are the best!
## Short description of the problem
Running `anvi-cluster-contigs` with `DASTool `or `Binsanity `as dri…
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_Originally posted by @jamesc99 in https://github.com/PacificBiosciences/sawfish/issues/2#issuecomment-2310789812_
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Hi,
after running Sawfish v0.12.2, the previous error in #…