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Comment: Differential protein expression analysis
by
dsull
★
4.2k
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 …
Comment: Differential protein expression analysis
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Ribo
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Thank you!
Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values
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melissachua90
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I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values
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Gordon Smyth
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No, your code isn't correct. You are testing an intercept equal to zero instead of testing for a logFC. I wonder what comparison you were t…
Answer: Extract sequences from a fastq file by a list of IDs
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GenoMax
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Using `filterbyname.sh` from [**BBMap suite**][1]:
You need to include the `/1` in the header in your list file (here I am using the `nam…
Comment: Limma returned only positive logFC values
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melissachua90
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Yeah, I added the design matrix. `design <- model.matrix(~0+group)`. These are raw counts.
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
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Ayish
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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? …
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
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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…
Answer: How to handle NaN in emmax Kinship matrix?
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Thu
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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]
The most complete seems t…
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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
Comment: Extract sequences from a fastq file by a list of IDs
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Pierre Lindenbaum
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> but none of them work for me
https://meta.stackexchange.com/questions/147616/
Comment: Extract sequences from a fastq file by a list of IDs
by
Pierre Lindenbaum
154k
https://meta.stackexchange.com/questions/147616/
Comment: Extract sequences from a fastq file by a list of IDs
by
mhpakdel96
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I have tried this one before but the output file is empty
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