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Dear Dr Jombart,
I am hoping you might be able to help me. I have sucesfully used the multidna constructor algorithms in apex to combine sequence data from 2 gene regions into a single matrix. This i…
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Hi, im trying to generate a genome index with STAR and while the log shows no errors, half of the files are not there.
Under the same parameters other genomes run just fine.
Any help will be apprec…
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Hi there, I was having the same problem in #933 and the fix below isn't working from the files from NCBI here: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/
> Both specifying the column o…
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Hello,
I'm running this workflow:
```golang
param (
// S3 path to 10x folder
tenx string
// Full s3 file location to put the sourmash signature
output string
//…
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I'm trying to compress a DNA sequence file and it throws a nullpointer. Any ideas why?
```
java -version
openjdk version "1.8.0_242"
OpenJDK Runtime Environment (build 1.8.0_242-b08)
OpenJDK 64…
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As more folks get sequence data back we have run into the issue of "blank" samples messing up the pipeline. These are samples that are run through the wet lab process with no DNA to test for contamina…
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The new version of CUDASW 4.0 claims to support only protein chains.
What needs to be done to be able to search in the nucleotide database?
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This input json file references two files that are in a private bucket:
https://github.com/broadinstitute/warp/blob/599f119c0220930bca8667bb7539d4bf81edcf06/pipelines/broad/dna_seq/germline/single_sa…
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v2 implemented transfering of partitioned files. Partition sizes could be specified, and there was an automatic algorithm to pick partition sizes based on the file size. This was never used, but it …
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```
What steps will reproduce the problem?
1.
Download Homo_sapiens.GRCh37.60.dna.toplevel.fa.gz from
ftp://ftp.ensembl.org/pub/current/fasta/homo_sapiens/dna/
2.
MosaikBuild -fr Homo_sapiens.GRCh37.…