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Got this error with TRBV18 and TRBV25
/Users/max2/anaconda3/envs/tcrdist3/lib/python3.8/site-packages/tcrdist/repertoire.py:466: UserWarning: TRBV18*01 gene was not recognized in reference db no cd…
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Bruno is using the following scripts to load the sweet cherry genome and gene annotations. These scripts are more automated and compliant with EBI metadata. To be consistent with Epl, Gramene may want…
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Hi Oliver,
We are interested in pseudogenes in a Salmonella genome. My colleague has run bakta, but no pseudogenes are being detected. This is unexpected based on some other analyses we have carrie…
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Hello, everyone. When i use star to align the RNA seq date to human genome, the output of the unmapped.out.mate is always large, nd it unique mapped is about 70%. Is it normal?
STAR
--genomeDir $i…
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# Status
| Dataset | platform | fastq downloaded | samples.csv | fastq renamed/ concatenated | config.yml | pipeline success |
|--|--|--|--|--|--|--|
|zheng_zhang_2017 | smartseq2 | wait for EGA …
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The instructions to make a Gene ordering file is unclear.
can you please add a few words about the files needed : **your_reference.gtf** and **your_gen_pos.txt**
Thanks
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Hi Alex,
Thank you so much for your great tool!
I have a quick question concerning the STAR `--twopassMode Basic`.
Which strategy (STAR with or without `--twopassMode Basic`) would you recomm…
JJBio updated
2 years ago
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Key points for introduction:
- What are genome annotations? What type of features are included in genome annotations (protein-coding genes, pseudogenes, RNAs etc)? What sorts of things do biologists …
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I am unable to build a database that contains /pseudo genes, although the `prokka-genbank_to_fasta_db` function has a pseudo gene option
`--pseudo! Include /pseudo `
I am calling
`prokka-g…
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Hi,
I understand that this issue has been discussed several times, but I still can't find a solution for my own problem.
I am mapping 14 Arabidopsis RNA-seq samples with STAR-2.5.a, using the ENCOD…