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https://github.com/PapenfussLab/gridss
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In tests 2 and 3 the file `phased_bam.bam` is not created and Galaxy stumbles over metadata generation
```
setting metadata externally failed for HistoryDatasetAssociation 15: Traceback (most rec…
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Hello,
I am getting the following error on the visualization.py script, can you please advice, what may be the reason for this following error:
I clone the repository by running git clone --recur…
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The vcf can be used as annotation source for genexus.
Must contain minimal vcf header following specs: https://samtools.github.io/hts-specs/VCFv4.2.pdf
Must contain class and comments from the db
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with command exit status error 141 (pipe error)
when calling
bwa mem -t 8 -SP {fasta} {R1.fastq.gz} {R2.fastq.gz} | samtools view -bS > {library}.lane1.0.bam | cat
when
[f…
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Tools that should be installed and work:
- rsem-prepare-reference
- rsem-calculate-expression
- ref-eval-estimate-true-assembly
- rsem-eval-calculate-score
- ref-eval
- blat
- samtools
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need to test by capture stdout like described on http://stackoverflow.com/questions/29686331/in-python-testing-the-standard-output-of-a-function?rq=1
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## Description
FileNotFoundError: [Errno 2] No such file or directory: './data/write_test_rg.bam.bai'
While a new file `-@ 4` has been generated. This is a known bug when generating bam.bai file wit…
zztin updated
2 years ago
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Hi Xun，
I used IGV to check the breakpoints, and extracted the reads mapped within 150bp from TSD, assembled and compared them.（samtools）
Is there a way to assemble a more complete ERV, via disc…
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Hello,
using samtools v1.14 the bam supplied in the example seems to be invalid. Running the example code results in the following error:
```
[E::sam_hdr_sanitise] Malformed SAM header at line…