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Recent Replies
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…
Comment: How to check Burrows-Wheeler Aligner (BWA) version on my terminal?
by
appropiate
▴
30
That was embarrassingly simple, thanks!
Answer: How to get intersected variants between multiple vcf files?
by
Jeremy Leipzig
20k
i would use vt to normalize and decompose your vcfs first - that should put all the multiallelic events on different lines
https://genome.…
Answer: How to check Burrows-Wheeler Aligner (BWA) version on my terminal?
by
Dave Carlson
▴
870
Just run the `bwa` command without the `--version` flag:
> $ bwa
>
> Program: bwa (alignment via Burrows-Wheeler transformation) Ve…
Comment: Why are reads from a region of a gene but not recongined as a mapped reads>
by
Pierre Lindenbaum
147k
why a screenshot of samtools when you can just copy and paste the text. Save the planet.
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