-
```
I would like to have the statistics on this for the meeting. Can we start a
merge today? I am attaching a spreadsheet with all the lanes to merge (by TCGA
name, since maybe some samples have m…
-
```
Moiz,
Jia mentioned that we use an "other" directory at DCC for uploads. If you know
how to access this directory, would it be possible for you to copy the
following 9 GB file there for us?
/…
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```
Zack,
The number of mapped reads for Esteller data
(~huydinh/huydinh_research/Data/External/Esteller) are ridiculously small.
Then, I come back to their paper's method section and found out tha…
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```
looking at the flowcell analysis dirs, vcfs are taking up a huge amount of
space.
for 4 lanes of nomeseq totaled 1.8TB (all files)
of this 1.5TB were just the vcfs.
is there any reason this s…
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Dear Alex,
I'm using STAR for something it was not designed for, mapping reduced representation bisulfite sequencing reads to a pseudo reference genome. This goes really well. One trick I apply is to…
-
```
One of the primary pieces of information about a library is library type. I
would make this a column in the left hand library selection screen of ECCP
```
Original issue reported on code.google…
-
Hi, all
I wondering about the bcbio-nextgen's next plan.
I really hope to contribute the another workflow (like metagenome, de novo assembly, epigenome) in bcbio.
💃
hmkim updated
8 years ago
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The JSON data hub already includes a proposed "assay_type" identifier, but this should be formalized in the metadata spec, in order to clearly define what goes in there. "assay_type" gives more fine-g…
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```
As far as I can tell from the BAM spec, flag 0x0040 is supposed to correspond
to read1 from a read pair, while 0x0080 is supposed to correspond to read2.
But BSMAP doesn't seem to output it thi…
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Transition from the old `bedtools` + `ggplot2` visualization code to pure `annotatr`. In addition to having "less moving parts", the annotations in `annotatr` are much better than what I threw togethe…