User: Nish314

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Nish3140
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Posts by Nish314

<prev • 8 results • page 1 of 1 • next >
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Mixed Illumina Methylation data from EPIC and 450k
... I am analyzing some mixed methylation array data from EPIC and 450k arrays using Minfi and would like to know whether the two arrays can be combined using `combineArray()` function prior to initial QC and normalization. Please could you advise me on how to combine the array data without compromising ...
dna methylation epigenetics minfi written 2 days ago by Nish3140
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Comment: C: Running STAR on multiple replicates
... Ah silly me! Thank you! ...
written 14 days ago by Nish3140
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Running STAR on multiple replicates
... I have 2 samples with 3 replicates each having PE reads. If I run: STAR --genomeDir genomeDir/ \ --readFilesIn Sample1-rep1-read1,sample1-rep2-read1,sample1-rep3-read1, sample1-rep1-read2,sample1-rep2-read2,sample1-rep3-read2 --runThreadN 8 \ --outSAMtype BAM SortedByCo ...
rna-seq written 14 days ago by Nish3140 • updated 14 days ago by swbarnes29.2k
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Comment: C: Is trimming necessary for RNAseq?
... Thank you for sharing these articles, they are really helpful! ...
written 16 days ago by Nish3140
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Comment: C: Is trimming necessary for RNAseq?
... Is adapter contamination inferred from the presence of over-represented sequences? I don't have any over-represented sequences. ...
written 16 days ago by Nish3140
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Comment: C: Is trimming necessary for RNAseq?
... Ok, as I am not performing a de novo assembly, I will perform an alignment using the untrimmed reads first. ...
written 16 days ago by Nish3140
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Comment: C: Is trimming necessary for RNAseq?
... I have just checked the per tile sequence quality has a warning in a couple of my fastqc files along with sequence duplication and per base sequence content, but only a few tiles are yellow, is it safe to ignore these warnings? When I run trimmomatic on these reads the per tile sequence quality pass ...
written 16 days ago by Nish3140
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Is trimming necessary for RNAseq?
... I am performing quality control on some reads that have good FastQC metrics apart from duplication levels and per base sequence content. Is it necessary to trim these reads before alignment and downstream DE analysis, variant calling etc? I have read conflicting advice about trimming before RNAseq a ...
trimming rna-seq fastqc written 16 days ago by Nish3140

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