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Tutorial:
Building mosdepth on macOS
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multi-omics data integration: a case study with transcriptomics and genomics mutation data
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Ming Tommy Tang
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Tutorial:
TAPIS installation and usage
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updated 8 days ago by
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written 8 days ago by
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Answer: Trimmomatic .jar not included anymore?
by
Pierre Lindenbaum
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> The command I used to run trimmomatic is this java -jar /storage/home/sjw6257/tools/Trimmomatic-0.39/
java -jar argument should be a f…
Comment: Trimmomatic .jar not included anymore?
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petebio
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I am guessing that you actually downloaded the source files and not the compiled binary which is why you are missing the .jar file?
If this…
Answer: Highly inflated p-values in GWAS by regenie
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SushiRoll
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Hi! Just jumping in with a suggestion rather than an answer, could it be that the p-values you're getting are not adjusted for multiple com…
Comment: kallisto normalized TPM values without bootstraps
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Thank you! Not really sure why I assumed the values had to come from sleuth, but tximport/DESeq2 worked great!
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before we dive in too deep let's confirm we are on the same page that gnomad 2.1.1 (in your text) is in hg37. gnomad 3.1.2 (in your screens…
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related: https://www.biostars.org/p/49627
Comment: Finding sequences in unannotated genomes using reference coordinates
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All done! Thanks.
Comment: Finding sequences in unannotated genomes using reference coordinates
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Please review all your previous questions and comment or validate them (green tick on the left) : https://www.biostars.org/p/9568243 https…
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langziv
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How is it possible to tell in case of a mis assembly?
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I was able to remove the warnings (which eventually ended up in an error) by creating transcriptome file from the genome and it's annotatio…
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Are you a student or employe at a university or research institute? In this case it is worth checking with your IT department if there is a…
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I think you should kill one of the processes, possibly the decoy one. Also keep an eye on the CPU temperature and the kernel_task. If CPU u…
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We use the OmniATAC protocol, which is an enhanced version. Celltype usually does not matter. Based on many years with this assay I can say…
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vk
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We used U2OS cells and followed the protocol given [here](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/).
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You could also do transcriptome assembly and then map the transcripts on the annotation via MAKER that will add an AED score for concordanc…
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