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Recent Replies
Comment: Clustering and dynamic tree cutting
by
harish
•
0
These are differentially expressed genes, which are around 15K genes from a total of 30 K genes. Then I follow the clustering protocol as g…
Comment: ceres score in crispr screen
by
edus_bioinfo
▴
20
I solved the issue with using bowtie. But now I am experiencing this issue;
> Error in makeGRangesFromDataFrame(., seqinfo = genomeinfo, k…
Comment: Protein protein interactions
by
Peerzada
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0
Sir, How much time does this server take to give output for 1 pair of proteins as I have submitted several hours ago and it still shows ru…
Comment: Question on how to filter DESeq2 results correctly and use of the results functi
by
Frederik
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Thanks alot :)
Comment: Is it possible to do bedtools multicov across the entire genome?
by
amy__
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Amazing, thank you so much!
BW,
Amy
Answer: Is it possible to do bedtools multicov across the entire genome?
by
GenoMax
125k
`mosdepth` ([**LINK**][1]) is an excellent/fast alternative.
[1]: https://github.com/brentp/mosdepth
Answer: Index with unmasked or masked in HISAT2
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GenoMax
125k
Use `top level` file.
See [**README**][1] more information about other files you are referring to.
[1]: https://ftp.ebi.ac.uk/en…
Answer: Is it possible to do bedtools multicov across the entire genome?
by
Nicolas Rosewick
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Simply use then `bedtools genomecov` with `-d` parameter : https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
Answer: How to enable multiple cores/threads for Bowtie2 or BWA using Macbook M2 chip?
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GenoMax
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Programs do not use all the threads/cores all the time. They will do so during appropriate part of the analysis. As long as you have enable…
Comment: Clustering and dynamic tree cutting
by
andres.firrincieli
3.1k
Help me to understand. Is this a clustering analysis of differentially expressed genes or an unsupervised clustering analysis (eg WGCNA)?
Answer: Obtaining every"Protein ID" from a genome in OMA
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Adrian Altenhoff
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Dear Christy,
thanks for your interest in the OMA browser. indeed, there seems to be an issue with listing all the genes of a species. W…
Answer: Error, (in LoadSpliceMap) string to parse is too long
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Adrian Altenhoff
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Dear Ziqing
this error seems to be related to the splicing information file of one of the genomes. Given that it worked previously, I as…
Comment: RNA Editing data from RNA-seq
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i.sudbery
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RNA editing is detected by identifying differences between the DNA sequence and the RNAseq. If you compare your RNAseq data to the referen…
Comment: How to find the most frequent alternative-splicing event from DEXSEQ data?
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i.sudbery
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DEXSeq is probably not the correct tool for what you are trying to do. If focuses of changes to which exons are included and which exclude…
Answer: How to use CAFE from Orthofinder Results
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dariober
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I have been looking into something similar (maybe, not sure myself) and I didn't know about cafe. It looks good, thanks for bringing it up.…
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