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Recent Replies
Comment: Calculation method of RMSMappingQuality
by
zhangfish
▴
40
Maybe, I think the formal (1) is correct for most situations (for example the earlier version of GATK). However, there are some changes in …
Answer: error in downloading of some accesions with fastq-dump
by
Utpal
•
0
Hi,
could you please let me know how to upgrade sratoolkit in centos?
Thanks and regards,
Answer: How to get fraction of unspliced reads for specific gene from scRNAseq Cell Rang
by
benformatics
3.5k
I don't think you can get that information specifically:
https://kb.10xgenomics.com/hc/en-us/articles/360021902671-Can-we-detect-splice-va…
Answer: Problem with fatsq-dump
by
Utpal
•
0
with the command
which fastq-dump
it returns:
~/.conda/envs/sratoolkit_env/bin/fastq-dump
Thanks.
Answer: Problem running interproscan-5.15-54.0 for protein sequences
by
Pratyay
•
0
Hi, can you guide me how to compile the src folder?
Many thanks!
Comment: Matching gene-expression data with clinical data: best practices.
by
krushnach80
★
1.1k
You can check [this][1]
[1]: https://www.linkedomics.org/
Answer: Matching gene-expression data with clinical data: best practices.
by
jose.sgomez94
•
0
Figured out one can use the TCGAutils package in R and UUIDtobarcode() function. Still, suggestions of best practices would be awesome!
Answer: Understanding multifactor designs and control variables in DESeq2
by
FrankStarling
▴
50
https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2021/RNAseq/Markdowns/10_DE_analysis_with_DESeq2.Solutions.html
…
Comment: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
by
Adaline.D
•
0
I appreciate your help, LChart! I will use raw data in case of a substantial loss of power.
(1) The publication did a PCA and then analy…
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
by
LChart
2.2k
Short answer: use LIMMA
Long answer: edgeR uses a negative binomial model, and expects *counts* and not *values*. Please read section 2.8.…
Comment: Python formatting when visualizing Primer3-py dimers
by
bhumm
▴
30
Wayne, both of these methods work beautifully. I really appreciate the detail you provided, thank you so much for your help!
Comment: Ortholog assembly and extraction
by
dthorbur
▴
420
I really like `orthofinder` and use it frequently, but there are also plenty of other tools out there. [Here](https://academic.oup.com/mbe/…
Answer: Cellranger sequencing
by
ATpoint
70k
Not that I am aware of. Unlike methods such as salmon it does genome alignment and does not resolve the exact transcript expression composi…
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