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For some reason there was an IndexError when running the method below, but since the variable `codon_alignment` was never initialized there was a UnboundLocalError raised as well claiming: _local vari…
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When aligning proteins with paralogs located in a cluster, `miniprot` produces alignments encompassing two or more distinct genes.
For example, aligning mouse protein NP_001036176.1 to human chrom…
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Hi Felix,
I have a couple of questions regarding Bismark. I'm sorry if they are stupid questions; I am fairly new to WGBS data and Bismark analysis (or to bioinformatics in general).
We are rese…
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Howdy!
I have an issue with the whatshap about not having the same number of reads. Here is the error.
[M::main] CMD: minimap2 -a -x map-ont -t 30 --secondary=no /project/hwwgru_mhk/jpf/prtus…
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Note sure what the error status means. I tried running the default test bam files
refdata_path=/home/mai/Desktop/svclin/clinsv
input_path=/home/mai/Desktop/svclin/bam_files
project_folder=/home/…
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Hello,
I have implemented RNA-Bloom on a subset of the PacBio bulk transcriptomic data and achieved the expected results. However, I noticed that some steps in RNA-Bloom take a considerable amount …
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**Are you using the latest release?**
yes
**Describe the bug**
I have been running several funannotate update jobs in parallel and I get an error in earlier steps. It is strange because sometimes…
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Is strobealign a good basis for the following application:
We would align against a pangenome FASTA. So we might have 100 genomes in this system. Downstream we project the alignments into a graph f…
ekg updated
11 months ago
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Hi,
Thank you for developing such an amazing tool to identify gene fusion from RNASeq data. I have 30 cancer sample Toral RNASeq data and 10 Benign sample Total RNASeq data. My focus is to identify …
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**Are you using the latest release?**
Yes, version 1.8.16 as installed per https://funannotate.readthedocs.io/en/latest/install.html via conda.
**Describe the bug**
Funannotate train generates a …