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Hi,
I am trying to utilize seqtk in order to convert quality score encoding of raw FASTQ files from illumina 1.5 to Sanger / illumina 1.9
my command line was:
seqtk seq -VQ64 inputfile-illumina1.5…
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Hello, I runned the following command :
`java -Xmx64G -jar pilon-1.24.jar --genome nano.fasta --frags illumina.sorted.bam --changes --fix all `
But the script end before with the following prob…
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### Context
https://github.com/AlexsLemonade/refinebio/pull/2844#issuecomment-885836634
### Problem
In the Illumina processor we have made some decisions that end-users should know about when t…
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### Is there an existing issue for this?
- [X] I have searched the existing issues
### Description of the Bug/Issue
Hi all,
First, thanks for all the work being done on this pipeline.
I'm ha…
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https://github.com/Illumina/ExpansionHunterDenovo/blob/998fd79587072153f53d2d4abc4c9f265777518e/scripts/core/common.py#L125-L128
From what I am reading the Bonferroni correction is the pvalue divid…
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Hi Alex,
`star-2.7.9a`
It appears that `--readFilesManifest` does not like a mix of single and paired reads. If I run using a manifest of all of one type it works fine. Below is what my manifest loo…
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display only *smarter* coordinates in variant detail endpoint. This could be done by creating a new collection with only the information I need. This collection will be served by the endpoint.
- [ …
bunop updated
4 weeks ago
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Processed fine but platform is incorrect (Illumina MiSeq not Illumina). Raises no error but fails EBI submission....(study ID 1696)
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**I do have any error when I run this command below and obtain the error**
![微信截图_20230215162258](https://user-images.githubusercontent.com/71307882/218973611-55ab2704-33bd-41a7-8dda-462c554b636f.png…
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[SeqPrep](https://github.com/jstjohn/SeqPrep) merges overlapping paired-end fastq files. It bumps up quality scores in overlapping scores accordingly (i.e. two agreeing bases with Q30 result in a Q60 …