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Sharon
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2.1 years ago by
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Recent Replies
Comment: Resolving over clustered NGS with Q-scores
by
sam.himes92
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The system that we used was [Aviti][1]. Our sequencing core was the one who quantified the loading/library concentration. Sorry I don't hav…
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Alex Reynolds
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I modified the answer with an approach for that use case.
Comment: Where can I get a list of SNPs mapping overlapping genes in humans?
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Ram
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OP is looking for overlapping genes - genes with presumably different gene IDs that share some loci. I think the `genes.bed` creation logic…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans?
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Note: The file `snps.bed` will be very large. You'll need sufficient disk space for this step.
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
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Alex Reynolds
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Given files `genes.bed` and `snps.bed`, you could do something like:
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$ bedmap --echo --echo-map-id --delim '\t' genes.bed snps.bed > a…
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You can use [AGAT][1] to process your annotation file to add the missing exons. I believe `agat_convert_sp_gxf2gxf.pl -g no_exons.gff -o wi…
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and you got answer that should be validate (green tick), or people asked you questions but got no answers.
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you asked questions before: review, comment and/or validate them please: https://www.biostars.org/p/9530777/ ; https://www.biostars.org/p/9…
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Thanks, Jared. Sounds like rounding counts is the simplest approach for now. :)
Comment: Resolving over clustered NGS with Q-scores
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Trivas
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Could you tell us which sequencer you used, how you quantified your library size and concentration, and what your loading concentration was…
Comment: Resolving over clustered NGS with Q-scores
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sam.himes92
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I should have mentioned, we ran both Read 1 and 2 well past the points of interest. For each read we ran 75 cycles.
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It might be because Illumina recommends 26 cycles for Read 1: https://knowledge.illumina.com/instrumentation/general/instrumentation-genera…
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ATpoint
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Has phiX been spiked in to increase nucleotide diversity.
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