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Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
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Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
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A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
Answer: Getting Intron Positions from Amino Acid Sequences
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Comment: How to deal with the probe id mapping to multiple gene ids?
by
GenoMax
127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
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rpolicastro
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`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created
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DdogBoss
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Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals
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YL
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Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals
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YL
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Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate
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ATpoint
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Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
Comment: Gene duplicate
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Ram
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> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis
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rpolicastro
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What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files
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Darrenjdd
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Perfect! Thank you!
Comment: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
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Daniel
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Hi, I am wondering if you ever got an answer for this question. Also, I am curious why it is true that "All the reads coming from one end…
Answer: how can i filter a sam file from a paf file
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Trivas
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A quick search shows that `paf2sam` doesn't exist because a `.paf` file doesn't contain the CIGAR strings that `.sam` files have. A work ar…
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Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: What is the major problem with this pipeline of SNPs analysis?
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Pierre Lindenbaum
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you can stick to gatk. But, again, using a GVCF without GenotypeGVCF is meaningless
Comment: Getting Intron Positions from Amino Acid Sequences
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fafad046
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thank you so so much, it worked! you are an absolute life savior :D
Answer: Getting Intron Positions from Amino Acid Sequences
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GenoMax
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Using [**EntrezDirect**][1] (truncated because of space): $ esearch -db protein -query NP_001243728.1 | elink -target gene | efetch …
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