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Recent Replies
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Thanks for sharing ! It seems there is a problem to install on Kaggle cloud (like a Colab): I tried several ways: https://www.kaggle.com/co…
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I am not sure what you gain by using hard masked genome for RNA-Seq mapping. There will be reads covering some introns. But if you mask rep…
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Thanks a lot, it works
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I don't have a tutorial but see this paper I co-authored:
https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00666
All of the upstream …
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Thank you!
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I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
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No, your code isn't correct. You are testing one group mean equal to zero instead of testing for differences between two groups. I wonder w…
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Using `filterbyname.sh` from [**BBMap suite**][1]:
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Thank you for reply. I have Illumina paired-end reads. Would it be fine if I use hard-masking for STAR and soft-masked genome for BRAKER2? …
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Soft masking the genome (unless something changed) not make any difference for STAR. Depending on how your RNA-Seq is done (Illumina? paire…
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Hi! Thanks for sharing your solution!
It works!
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Looks like there are five Clarias genomes:
* https://www.ncbi.nlm.nih.gov/genome/?term=txid13012[Organism:exp]
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Again, thank you so much for these very clearly explained summaries. After reading some articles on the matter, i feel i have a much better…
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Some people I know have used filter-fastq successfully: https://github.com/Floor-Lab/filter-fastq
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