User: prameelaawale

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Posts by prameelaawale

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Extracting Split read alignments
... I am trying to extract the split read alignments with bwa-mem for pair end sequencing. This is my code. # Extract the split-read alignments samtools view -h rscm2.bam \ | scripts/extractSplitReads_BwaMem -i stdin \ | samtools view -Sb - \ > rscm2.splitters.unsorted.b ...
alignment written 9 months ago by prameelaawale0 • updated 9 months ago by Pierre Lindenbaum131k
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## Help needed to run Lumpy with pair end discordant reads
... Hello everyone. I am trying to use this code below to run Lumpy for pair end discordant file. -pe bam_file:, id:, histo_file:, mean:, stdev:, read_length:, min_non_overlap:, discordant_ ...
next-gen sequencing written 9 months ago by prameelaawale0 • updated 9 months ago by ATpoint41k
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Differential expression analysis using DESeq2
... Hello everyone: I am new in using DEseq2. I am trying to analyze differential expression data using a publicly available data for my final project. It consists of 3 replications of control and three replications for treatment. I am trying to compare differential gene expression between treatment and ...
rna-seq written 19 months ago by prameelaawale0 • updated 19 months ago by genomax92k

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