User: prathyushareddy87

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Posts by prathyushareddy87

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Comment: C: STAR Unmapped reads
... I am just wondering if i be liberal with the STAR parameters would I be able to improve my mapping? But again I understand that if the quantity used or quality of RNA used is bad that might be causing this. I have samples processed using different library protocol kits (Illumina RNA Exome, Lexogen Q ...
written 3 months ago by prathyushareddy870
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Comment: C: STAR Unmapped reads
... I am not sure how to deal with % of reads unmapped: too short | 16.49%. I am wondering if there is any parameter in the STAR aligner that I could use to improve the % of unmapped reads. ...
written 3 months ago by prathyushareddy870
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Comment: C: STAR Unmapped reads
... Thank you so much for your feedback and comments. I would try to align my fastq files without headcropping to the reference genome if that could improve mapping and also not loosing good data. I have tried head command on out.mate1 files and those are fastq files. I will run blast on these fastq fil ...
written 3 months ago by prathyushareddy870
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Comment: C: STAR Unmapped reads
... I am pasting my STAR output here. Started job on | 4/22/18 3:57 Started mapping on | 4/22/18 3:58 Finished on | 4/22/18 4:00 Mapping speed, Million of reads per hour | 542.18 Number of input reads | 16867704 Average input read length | 209 UNIQUE READS: Uniq ...
written 3 months ago by prathyushareddy870 • updated 3 months ago by Devon Ryan82k
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Comment: C: STAR Unmapped reads
... Hi Devon, Here is my fastqc report. The input read length is 2*150bp length. I am unable to paste the fasqc image here. The mean quality value starts from 30 and goes to 40 and it is a straight line from there without any platos. I see a plato from 30 to 40 fro 10 bp. So, I have headcropped the 10 r ...
written 3 months ago by prathyushareddy870
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STAR Unmapped reads
... Hi all, I am newbie working on RNA-Seq analysis. I have samples processed using Illumina RNA Exome and Illumina TrueSEq librray protocols Paired end. I initially dif the qulaity control and I dont see any adpater contamination. I trimmed first 15 random reads and performed alignment step using STAR ...
unmapped reads alignment star rna-seq written 3 months ago by prathyushareddy870
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Missing samples (observations) in time series data
... Hi all, I am trying to find the differential expressed genes for a dataset where the samples are treated with a drug at three different time-points(baseline, 16 weeks, 52 weeks). There are no controls in the study. I am trying to use the limma in R and analyze this as they are paired samples. I am ...
timeseries microarray limma written 9 months ago by prathyushareddy870 • updated 8 months ago by Kevin Blighe26k
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Filtering low intensity probes of microarray data
... Hi All, I have a question related to the analysis of the microarray data. In the process of differential gene expression analysis, filtering low probe intensities is very crucial. The array chip I am analyzing presently is HuGene1.0 ST array. I am using oligo package in R to analyze and rma normali ...
R written 12 months ago by prathyushareddy870 • updated 12 months ago by h.mon18k

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