10xgenomics / longranger Goto Github PK

Hi,
What do you thing about packaging longranger in Conda package by comiting into the BioConda repository
Best regards

Dear all,
I am using longranger align for mapping tetraploid plant samples (10x reads) (Potato-tetraploid) on my reference. Overall alignment rate is 95%.
For variant calling i am interested in choosing properly paired end reads and in my case its too low (67.35%).
Why longranger reports low properly paired end reads and whats the mechanism /algorithm behind reporting these reads)? Is there any other better option for aligning 10x linked reads?
Secondly longranger wgs works for tetraploid samples as well? Because I normaly use freebayes separately to call variants across all samples as I have both diploid and tetraploid samples.

How does it take to run longranger wgs on a mouse genome?

Hi,
How can we create a reference genome with longer contigs??

$ go version
go version go1.16.3 linux/amd64
$ git log --oneline -1
e2a3143 (HEAD -> master, origin/master, origin/HEAD) update LICENSE
$ make
go install -ldflags "-X loupe/goloupe.__VERSION__ 'e2a3143'" loupe/goloupe
go install: version is required when current directory is not in a module
	Try 'go install loupe/goloupe@latest' to install the latest version
make: *** [Makefile:56: loupe/goloupe] Error 1

The suggested command also fails:

$ go install loupe/goloupe@latest
go install loupe/goloupe@latest: malformed module path "loupe/goloupe": missing dot in first path element