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Recent Replies
Comment: Subset Seurat object from Xenium spatial data
by
bk11
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For subsetting a sample, you can do something like this-
Idents(seuratObj) <- "orig.ident"
subj1 <- c("subject_1")
subj1_seur…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
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Ok! I have a recommendation. I'll submit it as an answer, pending your feedback.
vincent
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anasjamshed
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In modeller we need to use templates as well.so 63% is acceptable
Comment: DYH17 Structure Prediction
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Mensur said
> The latter option assumes you know how to use Modeller
Do you know how to use Modeller? I vaguely recall there being a mini…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
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GenoMax
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OP is working with long reads so the chances of reads aligning to unlocalized scaffolds are relatively small. Doing some testing may be suf…
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
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I personally think that comparing the same peak between conditions is meaningful and comparing peaks within the same sample is not.
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
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ATpoint
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These regions are present in the genome and removing them might incorrectly redirect alignments to known genes. I don't see why you would r…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
njornet
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Ok thank you! Do you know if there is an easy way of doing so with ncbi-genome-download or I need to use another tool?
Comment: Using vg gamsort with naive sorting algorithm
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> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Redirection of Duplicate PMIDs
by
dominickd
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The scope is all publications related to grants from an NIH award program. There are currently ~120k publications in total (about a few hun…
Answer: Using vg gamsort with naive sorting algorithm
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The `-d` sorting mode does the entire sort in memory, so it will only work if you have enough memory to load your whole GAM file.
To fin…
Comment: Redirection of Duplicate PMIDs
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dominickd
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I have a list of PMIDs for publications linked to a list of grants, exported from NIH RePORTER.
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> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
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Yes you can remove those if you are only interested in annotated genes.
Comment: Help for coding: Trinity for differential gene expression studies
by
mchour
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[This could help][1]
[1]: https://github.com/trinityrnaseq/RNASeq_Trinity_Tuxedo_Workshop/wiki/Trinity-De-novo-Transcriptome-Assembly-W…
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