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Comment: How to reduce the variation of CIBERSORTx results?
by
feather-W
• 0
Hi LChart, Thanks for your reply. I see S-mode in the CIBERSORTx official website tutorial(https://cibersortx.stanford.edu/), and the imag…
Comment: How to reduce the variation of CIBERSORTx results?
by
LChart
3.9k
First time I've heard of S-mode. I imagine you've seen this benchmark where it doesn't come out too well: https://academic.oup.com/bib/arti…
Comment: ISCN annotation for SV/CN VCF files
by
adedare
• 0
https://res.saletool.cn/vcf/18084521725806
Comment: ISCN annotation for SV/CN VCF files
by
adedare
• 0
https://res.saletool.cn/vcf/18084435127462
Comment: How can I solve this error?
by
22211020193
• 0
I want to conduct GWAS meta-analysis using metal software.
Comment: How to reduce the variation of CIBERSORTx results?
by
feather-W
• 0
Hi LChart, Thanks for your reply. Yes, the identical command lines produce different results in CIBERSORTx S-mode. Although I input the da…
Comment: Removing duplicates
by
joe
▴ 490
I *could* imagine an ONT scenario where you'd want to remove duplicates (amplicon-seq, etc) but likely for variant calling there is no need…
Comment: Removing duplicates
by
samuel.a.odonnell
▴ 510
As above, you do not need to worry about duplicates for ONT data Also have you looked at using other tools for variant calling more suited…
Answer: Pediococcus acidilactici sequence analysis
by
geneontologyhelp
▴ 340
If you're looking for the GO annotations for *Pediococcus acidilactici*, these are available. Using the instructions under [*2. All other…
Answer: What is the normalization status of metabric data?
by
etiennedanis
▴ 10
I just found an answer to this question here: [https://groups.google.com/g/cbioportal/c/hm_i4jbG1uc/m/h9rNYOvpAAAJ][1] [1]: https://gro…
Comment: Removing duplicates
by
joe
▴ 490
With ONT you will only have PCR duplicates. 'Read' (you mean optical?) duplicates are an artifact of cluster-based sequencing (ie Illumina)…
Comment: assembly using CCS, CLR, CCS_CLR sequences together?
by
GenoMax
141k
PacBio has some recommendations on software for genome assemblies on this page (which you may have seen but just in case): https://www.pacb…
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…
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