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Forum:
Survey for job context
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What bioinformatic training?
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An idea for a project in ML
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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
by
Ribo
▴
40
Thank you!
Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values
by
melissachua90
▴
40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values
by
Gordon Smyth
★
6.1k
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
by
GenoMax
129k
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
by
melissachua90
▴
40
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
by
Ayish
•
0
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
by
Darked89
4.4k
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?
by
Thu
•
0
Hi! Thanks for sharing your solution!
It works!
:)
Comment: Gene prediction software
by
Darked89
4.4k
Looks like there are five Clarias genomes:
* https://www.ncbi.nlm.nih.gov/genome/?term=txid13012[Organism:exp]
The most complete seems t…
Comment: Alignment of case vs. control from different origin
by
sativus
▴
10
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…
Answer: Extract sequences from a fastq file by a list of IDs
by
colindaven
4.9k
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
by
Pierre Lindenbaum
154k
> 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
•
0
I have tried this one before but the output file is empty
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