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Recent Replies
Comment: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
by
seidel
11k
What technology is the GEO data set derived from? Signal intensity implies a fluorescence read out (i.e. microarray). If that's the case, y…
Comment: Log2 FC Threshold
by
seidel
11k
Given that 0.2 is a 1.15 fold change (2^0.2) you're right to be skeptical, but there's no clear answer as to the significance. Consider tha…
Comment: Read lengths greater than insert length
by
GenoMax
127k
As I said above the adapters are each ~60 bp long so they add ~120 bp (5' and 3' end adapters) to the length of the DNA fragment. What you …
Comment: Problem with fatsq-dump
by
GenoMax
127k
Looks like the developers have an answer for this error: https://github.com/ncbi/sra-tools/issues/139
At least the program seems to be ins…
Comment: Read lengths greater than insert length
by
shpak.max
▴
30
I'm not claiming that all fragment lengths are exactly 50, the typical range for my data is 45-60. However, my read lengths are all 150, so…
Answer: Read lengths greater than insert length
by
GenoMax
127k
Illumina libraries are made by adding adapters to the ends of DNA fragment(s). Those adapters themselves are about 60 nucleotides long. Not…
Answer: How to get fraction of unspliced reads for specific gene from scRNAseq Cell Rang
by
Rob
5.9k
If you have the raw data, you can easily get this information using [alevin-fry](https://www.nature.com/articles/s41592-022-01408-3). It pr…
Answer: Matching gene-expression data with clinical data: best practices.
by
pilargmarch
▴
60
I really like using [the R/Bioconductor package TCGAbiolinks][1], it gives you clinical and expression data by patient ID.
[1]: http…
Comment: Problem with fatsq-dump
by
Utpal
•
0
with the command
which fastq-dump
it returns:
~/.conda/envs/sratoolkit_env/bin/fastq-dump
With fastq-dump I get the following error …
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 …
Comment: 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…
Comment: 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/
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