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P. evermanni has two miRNAs that have been assigned the name "peve-mir-novel-4", rows 21 and 22 of the [csv](https://github.com/urol-e5/deep-dive/blob/main/DEF-cross-species/output/10-shortRNA-ShortSt…
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Hi miRge development team,
My Institute have a new installation of miRge2.0, which followed the installation using Bioconda. We found a missing file when trying to use 'Predict' mode:
line 647,…
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Here I'd like to open the discussion on the use of the "star" symbol.
Originally, when we thought that only one arm of the hairpin was functional, the star symbol (_) was used to convey that this str…
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I'm trying to use 'gdcParseMetadata()' to parse metadata by providing the metadata file, but find that the format of the metadata file in GDC has been change recently.
So, I want to know how long th…
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The following relations do not have textual definitions. Some seem obvious by their labels, but I never trust that. I'll be trying to define these based on the paper and citation tracking, but contrib…
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Hi All,
I have been trying to use miRA for miRNA analysis and to find novel miRNAs in Ipomoea batatas.
The command I am using is:
./miRA full -c configuration.config bam_files/SpR_Ctrl.sam Ref_genome.…
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```
% ./bin/taffy view --region=Anc0refChr0:10-100 < tests/dupe_test.maf
#taf version:1 scoring:N/A
Segmentation fault (core dumped)
```
It would be useful to be able to select regions from …
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I wanted to transform the **gff** (`ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/reference/GCF_000001405.38_GRCh38.p12/GCF_000001405.38_GRCh38.p12_genomic.gff.gz`) to **…
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The fake negative entrez gene IDs give us a lot of headache. Let me document how we generate them here and see if we can solve the issue.
The mirna id file reside in the id-mapping-mirbase.txt file…
jjgao updated
5 years ago