-
This is more a usage question than an issue. I have a converged run, based on ~30x 100bp PE sequencing. The genome size estimate I get is ~527MB. From related spp and flow cytometry I know the real ge…
-
I’m running the preprocessing part of the pipeline for the first time on a full dataset on a cluster node. So far, only `bwa mem` uses all 16 cores. MarkDuplicates uses just one core, so does PrintRea…
-
This comes up in the performance test running on MacOS 10.8.5 compiled with i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00):
../../crux comet --p…
-
A typical routine for me after our processing / alignment pipelines are complete is to load up an interactive session on our painfully slow remote cluster and create a new SeqMonk project with the dat…
ewels updated
7 years ago
-
#109 highlighted some issues: namely, which tools to support tumor/paired calls.
There is a comprehensive list on BioStars (http://www.biostars.org/p/19104/), so the plan would be to evaluate which o…
-
This one is tricky, so I'm going to be thorough in the explanation.
## Problem
Exploration of the root cause of #1294 by @nanliu has found a noticeable conflict in naming conventions between the …
-
Hello,
I'm having an issue running crossmap on the human genome, specifically it seems like when it gets to the unlocalized or unplaced scaffolds. I have limited the dataset by not using the "alt" …
-
Hi Brad,
just a quick question. Is there a reason you omitted some VEP annotation options during that step?
Wouldn't it be possible to just use the "--everything" option to maximize the annotations …
-
Hi Brandon,
I found something unexpected when plotted out metagene profiles using included IPy-notebook file "create-orf-type-metagene-profiles.ipynb" by using my own data from yeast.
Most of …
-
Hi Brad,
We're experiencing a huge slowdown of the analysis while calculating the coverage bins.
Command executed:
```
[2016-09-30T08:44Z] /home/galaxy/bcbio/galaxy/../anaconda/bin/samtools depth -…