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Tutorial:
Gene Set Enrichment Analysis
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Hamid Ghaedi
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updated 20 days ago by
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Ram
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updated 22 days ago by
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Kevin Blighe
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Tutorial:
Parsing HMMER output
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Recent Replies
Comment: Removing duplicates
by
quentinperriere
•
0
thank you for responding.
I was looking for suitable variant calling tool. I'm working on fungus and I don't have fast5 files.
Could you re…
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
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0
https://res.saletool.cn/vcf/18084435127462
Comment: How can I solve this error?
by
22211020193
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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
▴
500
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
▴
520
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
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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
▴
500
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?
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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
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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 ??…
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