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from the mountains
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curious
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Pierre Lindenbaum
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Recent Replies
Comment: Chromosome bias on RNA-Seq differential gene expression analysis
by
blz
▴
20
It could be possible to observe an extra copy only in the knockout, it's a (pathogenic) plastic microorganism. But it's unlikely to happen …
Comment: Trimmomatic .jar not included anymore?
by
Pierre Lindenbaum
157k
please review all your previous questions and validate the correct answers (green tick on the left): https://www.biostars.org/p/9575583 htt…
Answer: Trimmomatic .jar not included anymore?
by
Pierre Lindenbaum
157k
> 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?
by
petebio
▴
80
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
by
SushiRoll
▴
110
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
by
butterman16
▴
20
Thank you! Not really sure why I assumed the values had to come from sleuth, but tximport/DESeq2 worked great!
Comment: Weirdness in annotation (missing allele frequencies)
by
Jeremy Leipzig
21k
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…
Comment: Finding sequences in unannotated genomes using reference coordinates
by
Pierre Lindenbaum
157k
related: https://www.biostars.org/p/49627
Comment: Finding sequences in unannotated genomes using reference coordinates
by
Prangan
▴
20
All done! Thanks.
Comment: Finding sequences in unannotated genomes using reference coordinates
by
Pierre Lindenbaum
157k
Please review all your previous questions and comment or validate them (green tick on the left) : https://www.biostars.org/p/9568243 https…
Comment: Dealing with transcriptome sequences that are smaller than their respective gene
by
langziv
▴
50
How is it possible to tell in case of a mis assembly?
Comment: Salmon alignment based quantification
by
Mat
▴
60
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…
Comment: Salmon index not progressing
by
Michael
53k
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…
Comment: Salmon index not progressing
by
Michael
53k
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…
Comment: ATAC-seq troubleshoot - Just Noise
by
ATpoint
76k
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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