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Recent Replies
Answer: GATK's selectVariants not outputting VCF
by
dec986
▴
340
The correct way to enter in the command to GATK's HaplotypeCaller is
`/usr/local/share/gatk-4.2.6.0/gatk --java-options '-Xmx4g' Haploty…
Comment: Trying to find file tutorial_8017 for GATK tutorial from the Broad Institute
by
appropiate
▴
30
Sorry I misread, and thought you meant Java. In Chrome settings it shows that sites can use Javascript.
Comment: Trying to find file tutorial_8017 for GATK tutorial from the Broad Institute
by
appropiate
▴
30
Great, thanks!
Comment: Trying to find file tutorial_8017 for GATK tutorial from the Broad Institute
by
appropiate
▴
30
Next to the edit button I have a "Following with messages" dropdown menu that does not include delete option. I tried Chrome and Firefox in…
Answer: Trying to find file tutorial_8017 for GATK tutorial from the Broad Institute
by
GenoMax
118k
This should get you the data you need:
$ wget -O tutorial_8017.tar.gz ftp://gsapubftp-anonymous@ftp.broadinstitute.org/tutorials/datas…
Comment: Are there any tools that automatically detect where to truncate forward and reve
by
O.rka
▴
610
I appreciate your help in this and your detailed explanation!
>DADA2 implemented via wrapper python scripts in QIIME2 or directly in R can…
Comment: Trying to find file tutorial_8017 for GATK tutorial from the Broad Institute
by
Ram
36k
Maybe your browser has JavaScript disabled? It should be right next to the `edit` button:
![screenshot][1]
[1]: https://i.ibb.co/G52XQvV…
Comment: Trying to find file tutorial_8017 for GATK tutorial from the Broad Institute
by
appropiate
▴
30
Thanks! I was trying to delete it myself, how could I do that? I do not see the "moderate" button to delete my posts, which I read about in…
Comment: Trying to find file tutorial_8017 for GATK tutorial from the Broad Institute
by
Ram
36k
[Your previous post][1] was marked as spam by the spambot owing to URLs in the title. I've removed it from spam and deleted it as a duplica…
Comment: Sudden drop in coverage in single-cell RNA-sequencing data
by
tien
▴
10
Hi, sorry for my bad question. This screenshot is not about my data but my data behaves the same and I did take umi into account when plott…
Comment: How to calculate position-specific fastq stats?
by
O.rka
▴
610
Thanks, that's good to know. I ended up writing one last night and updated the question.
Comment: Are upset plots bad for differential expression analysis?
by
paulimer
▴
10
> Whichever direction has the smallest product of p-values (i.e., which is more significant under a Fisher's method meta-analysis)?
That's…
Answer: Filtering multiple-samples VCF by genotype with GATK
by
LChart
▴
380
I think you either need to escape the inner quotes, or use single outer-quotes and double inner quotes
`'vc.getGenotype("sample1").isHom…
Answer: RNAseq matrix input for WGCNA analysis
by
LChart
▴
380
You should be able to pass in `$abundance` to WGCNA methods directly:
```
library(tximportData)
library(tximport)
library(WGCNA)
d…
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