User: sdalin

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sdalin0
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Posts by sdalin

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EdgeR: With two treatments, is it equivalent to split into two different models vs. making the relevant pairwise comparisons?
... I'm very new to edgeR, so this may be a silly question... I have a CRISPR screen with the following design:   + conditioned media - conditioned media + drug d.cm d.ncm - drug nd.cm nd.ncm There are three biological replicates of each of the four c ...
edger contrast design matrix written 11 months ago by sdalin0 • updated 11 months ago by Gordon Smyth39k
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ProcessAmplicons using very little memory on big job?
... I'm trying to use processAmplicons to generate sg counts for a CRISPR screen. I've got ~200 million reads per fastq file, with 4-5 barcodes per file, and 180000 guides.  I'm running this on my school's cluster which has ~30GB per node of the cluster.  When I submit one fastq for analysis, I request ...
edger processamplicons memory problem written 15 months ago by sdalin0
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Answer: A: EdgeR: run processAmplicons without barcodes
... Here is the work around that I ended up using:  Make a barcodefile with your sample ID, group, and replicate, and then a 2 base long barcode.  Can be anything.  Then when you call processAmplicons, set allowMismatch=TRUE and barcodeMismatchBase=2 This will make the barcode into any 2-mer, so every ...
written 17 months ago by sdalin0
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processAmplicons to match sequences 1 or 2 bases shorter than guides?
... I'm working on using processAmplicons to map my reads to my library's guides.  After talking to my department's bioinformatics core, they suggested allowing up to 2 mismatches, as well as 'truncated' matches, ie, the guides are 20 bases long, so an 18 or 19 base match.  Is there a way to map truncat ...
edger processamplicons written 17 months ago by sdalin0 • updated 17 months ago by shepherl ♦♦ 1.6k

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