-
```
Hi Zack,
Could you please run BAMs through a pipeline bisulfite-seq "merge" workflow,
which will generate Q/C and run Bis-SNP?
There are two BAMS located at :
~huydinh/huydinh_research/Data/ER…
-
This issue is a scratchpad of features and ideas on bioinformatics pipelines.
The pipeline's notion of a fastq should be parameterized by what it contains: DNA or RNA (from cDNA). This could allow us…
-
```
In pre-ECDP days, we had this very cool plot which showed sequence composition
counts by cycle. This can show fragmentation biases that appear at 5' ends, as
well as RNA-seq random priming bia…
-
```
We purchased a high end database server to store TCGA bisulfite-seq datasets.
We have had trouble getting HPCC to allow access from individual cluster nodes,
even though we cleared this with Ma…
-
```
download novoalign
install
try on bis data
```
Original issue reported on code.google.com by `zack...@gmail.com` on 4 May 2012 at 6:26
-
```
Many of the merges we started last week look incomplete, and I don't see lots
of analysis jobs still running. Do we know if these jobs are failing? Or some
problem with ECDP updating?
Here a…
-
```
cd /export/uec-gs1/laird/shared/production/ga/external_analysis
make a directory for your project (Ex: LijingAnalysis)
cd to ZackExome
mkdir a dir for your experiment (Ex: chipseq)
cd chipseq
ma…
-
```
Use specs laid out by David, Dan, Charlie, lab
DNA/RNA
- subtype
- DNA
- mRNA
- total RNA
- cDNA
- random primed
- oligoDT
- mtDNA
- chip DNA
- chroma…
-
Would it be possible to filter out reads with partial coverage - remove the reads that have "unknown" methylation status? It'd be useful for high-coverage BS-seq data sets where we want to plot speci…
timp0 updated
8 years ago
-
```
Today I saw there were samples with the appropriate analysis type in GENEUS but
not on the work flow params file.
```
Original issue reported on code.google.com by `cmnico...@gmail.com` on 26…