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Hi, there! I have used the stringtie2 to the genome-based transcripts assembly. I used the hisat2 to do the alignment of the RNA-seq data , and then the picard the remove the PCR errors. Finally, used…
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Workaround using the existing functionality: If I have, say `var_g` = `hgvs.parser.Parser().parse_hgvs_variant('NC_000005.9:g.112090651A>G')` and I want to do liftover between assemblies, one way that…
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My code:
```r
bamba_ret = bambu(
reads = bam_file,
annotations = gtf_file,
genome = fna_file,
quant = FALSE
)
```
The error:
```
Error in value[[3L]](cond): Input g…
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hi ,there
The scallop is a good software to assembly the illumina data and I got lots of transcripts that other softwares can not. When I use the ORFfinder to predict the ORF with the scallop resu…
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mitochondria large subunit
Systematic ID | Gene name | Product description | Budding yeast orthologs | Human orthologs
-- | -- | -- | -- | --
SPAC1610.02c | mrpl1 | mitochondrial ribosomal prot…
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Hello,
I noticed some abnormalities in the results of taco_refcomp (assembly.refcomp.gtf).
1. If I understand correctly, `category` column should be defining what the called transcript is, right…
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Previously, our team was not able to successfully output a gene count matrix from Stringtie. I was able to run Stringtie on Andromeda and output a gene count matrix but many of the rownames are design…
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Unconventional amino acid sequences cannot be correctly identified and output. For example, my amino acid sequence contains U, but the output result of this tool is "*", which leads to an unexpected g…
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Hi,
We have tried helixer on the Cupressus sempervirens genome assembly
https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_028749045.1/
but obtained poor busco results on the 38652 called transcrip…
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The rnaSpades mode is heavily focused on mRNA transcriptome assembly and is very aggressive at splicing assemblies into short transcripts. The —meta mode would be more suitable for our DNA/RNA assembl…