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Hi, I tried to annotate my genome with funannotate(v1.3.3). When I run the test run for the sample data, for all the genomes, it stopped at filtering out bad gene models
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[09:32 AM]: now filterin…
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I'm wondering if it would be possible to use UMI-tools to perform deduplication just based on read sequence. Let's consider a read with a 5nt-UMI followed by a DNA sequence of biological origin. It sh…
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Functional annotation was added to the gene models. These include `PFAM`, `InterPro` and `GO`.
It would be good to provide users with a link out to databases with information about these DB referen…
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Hello,
I have an issue running funannotate predict: `funannotate predict -i genome.cleaned.sorted.masked.fa -o predict/ --species "MySpecies" --transcript_evidence TSA/allmRNA.evidence.fa --protein…
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Hi,
Running Funannotate v1.3.2, I got and error in the Predicting tRNAs step:
File "/services/tools/anaconda2/4.4.0/lib/python2.7/subprocess.py", line 1025, in _execute_child
raise child_…
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Hi Jon,
Thanks for funannotate and for your continuing support!
I was running version 1.1.1 to annotate a fungal genome. It went well with beautiful results, but I got one warning which I would…
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Hello World,
I have been attempting to use Kallisto to analyse genes and transposable elements in tandem.
This requires creating a custom gtf file to be used for kallisto index. It seems as though…
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Reads will not be considered if they map to different locations on the reference with similar quality. This should take into account that sometimes only short regions of a read map to a different loca…
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**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?**
alevin
**Describe the bug**
I am trying to use Alevin to quantify a single cell RNA-Seq 10x Genomics CHROMIUM …
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Hi Felix,
I'm a regular user of bismark (actually I had post in seqanswer in the past a few times) and now I have a new set of data that I want to analyze.
As before, let me notice that my reads cam…