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A: Ribo-seq vs RNA-seq read count
C: What is the definition of "read depth" vs "coverage"? (again...)
C: What is the definition of "read depth" vs "coverage"? (again...)
Comment: Bwa sampe - BGI
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
Tools To Calculate Average Coverage For A Bam File?
Comment: Retrieve a % coverage for each transcript
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bk11
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Recent Replies
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
swbarnes2
14k
I would not put totally different tissues in the same DESeq object. I don't think that's going to do good things for normalization or disp…
Comment: Removing duplicates
by
quentinperriere
• 0
pcr duplicates or/and read duplicates should I use this command to remove them ? or we don't talk about duplicates when dealing with ONT ??…
Comment: How to reduce the variation of CIBERSORTx results?
by
LChart
3.9k
If you didn't change the input signature matrix, the input RNA matrix, or the input parameters - what did you change? Is the statement that…
Answer: Inconsistency in SNP detection pipelines for multi-sample analysis
by
LChart
3.9k
> To replicate GVCF behavior and avoid issues with 0/0 genotypes appearing as missing, I don't use the -v option I'm not sure what you m…
Comment: Supergnova stuck in tutorial
by
GenoMax
141k
Your best option may be to email the author (and/or the senior author from the paper). Let them know that the FTP links mentioned on GitHub…
Comment: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
BioinfGuru
★ 1.7k
Thanks @lchart, I accept that, I'll wait to see if there's any more who want to input and then accept the answer
Comment: Per base sequence content failed miserably
by
GenoMax
141k
What kind of data is this? Plain genomic/amplicons? How you proceed will largely depend on the context. Can you also post the original fast…
Comment: Removing duplicates
by
samuel.a.odonnell
▴ 510
I guess the enlightening question is: duplicates of what?
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
LChart
3.9k
I don't think this approach will give you what you want. Combining multiple tissues in the way you are suggesting will result in a positive…
Comment: Supergnova stuck in tutorial
by
Murat
• 0
Hi Gerard, I am also using the tutorial and found your answer. The ftp links are not working any longer; is there any other source to downl…
Comment: Method to detect genome doubling
by
Zhenyu Zhang
★ 1.2k
This is only true for pure WGD that is not distinguishable using NGS. However, in most tumor evolution, a WGD event is often followed b…
Comment: Questions about a bug when transferring cram file to bam file
by
Pierre Lindenbaum
161k
> Interesting, does this mean I cannot find the reference of this cram file? it means that the REF you're using is not the one that was …
Comment: How to get the reference panel for UKBB
by
bk11
★ 2.3k
Please check this link [here][1]: ![https://www.ukbiobank.ac.uk/enable-your-research/about-our-data/genetic-data][2] [1]: https://www.…
Comment: Retrieve a % coverage for each transcript
by
GenoMax
141k
Past threads that should be useful: https://www.biostars.org/p/287692/<br> https://www.biostars.org/p/9556576/
Comment: Can I readmap short reads to rDNA references?
by
aniigodwinn
• 0
Thank you! I will try this now.
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