billzt

I make a Cartfile in my base directory and write: ``` github "maximveksler/GeohashKit" ``` Then I run: carthage update --use-submodules It failed! It says: ``` usr/bin/xcrun xcodebuild -project /Users/zhutao/Documents/xcode/geohash/geohash/Carthage/Checkouts/GeohashKit/GeohashKit.xcodeproj -scheme...

How to use the json file with IGV, Biodiance, JBrowse

2

Well, the tool is really wonderful. But after I get the JSON file, how to use it with genome browsers such as IGV, Biodiance, JBrowse?

Why FASTQ quality value above qmax is treated as Fatal error?

6

When I used `--fastx_filter` to trim FASTQ files (seeming like a very easy task), ``` $ vsearch --fastx_filter in.fastq --fastq_stripleft 20 --fastq_stripright 20 --fastaout out.fa ``` I encountered Fatal error...

https://github.com/OpenGene/ctdna-pipeline/blob/master/pipeline.sh#L24 says: ```bash java -jar VarScan.v2.3.8.jar mpileup2snp outdir/test.dedup.mpileup --min-coverage 4 --min-reads2 2 --min-avg-qual 20 --min-var-freq 0.001 --min-freq-for-hom 90 --output-vcf 1 >outdir/test.snp.vcf ``` Now I'm not sure whether the value of...

This is the advise from one reviewee

How to understand the levels in the result file?

1

This is a row of my result ``` ;SeqID MislabeledLevel OriginalLabel ProposedLabel Confidence OriginalTaxonomyPath ProposedTaxonomyPath PerRankConfidence MN952976 Domain Pempheriformes 0.999 Metazoa;Chordata;Actinopteri;;Lactariidae;Lactarius;Lactarius lactarius Metazoa;Chordata;Actinopteri;Pempheriformes 0.999;0.999;0.999;0.999 ``` My question is: (1)Why the...