User: Genomics

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Genomics20
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Posts by Genomics

<prev • 11 results • page 1 of 2 • next >
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Probability of rare variants
... Hello all, I have sequencing data for a disorder in population. I found couple of LoF variants in sample. How should I calculate probability of how likely is this to occur by random chance? Also If I see 2 LoF variants in two different genes in a same individual how should i calculate probability. ...
probability variants statistics written 12 days ago by Genomics20
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Comment: A: Input file for CompareCluster in ClusterProfiler
... Thank you for the answer. It worked. Thanks alot. ...
written 6 months ago by Genomics20
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Input file for CompareCluster in ClusterProfiler
... Hello everyone. My questions might be naive but I would really like to know how should i prepare gcSample for CompareCluster. I have 3 analysis results and each of them is having around 2000 genes and I would like to plot keggenrich in one plot. I tried reading a text file x <- read.table("C:/U ...
clusterprofiler comparecluster written 6 months ago by Genomics20
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Comment: C: RNA Seq Analysis:Feature Counts are zero
... I've removed rRNA by mapping them to rRNA databse Also how about doing a Denovo assembly and checking where the reads are aligning? ...
written 9 months ago by Genomics20
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Comment: C: RNA Seq Analysis:Feature Counts are zero
... My samples are from swab, I've not done any lab work, just analyzing the data.But I can get RNA integrity. All CXCls have no counts in samples. ...
written 9 months ago by Genomics20
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Comment: C: RNA Seq Analysis:Feature Counts are zero
... Agreed to this point. But why am I getting aligned reads (12-20 M) for all samples. I want to know where are they going and aligning. ...
written 9 months ago by Genomics20
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Comment: C: RNA Seq Analysis:Feature Counts are zero
... I have visualized in IGV , it shows the same as what i get in feature Count. ...
written 9 months ago by Genomics20
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Comment: C: RNA Seq Analysis:Feature Counts are zero
... I did this. Doesn't help ...
written 9 months ago by Genomics20
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Comment: C: RNA Seq Analysis:Feature Counts are zero
... Yes it is matching my library is F/R strand and I've used following in Hisat --fr -1 ...
written 9 months ago by Genomics20
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Comment: C: RNA Seq Analysis:Feature Counts are zero
... Not all counts are zero, but for some specific genes i would expect counts to be higher in samples Following command i have used featureCounts -p -t exon -g gene_id -a Refseq.gtf -o output.txt sample.bam -M -O For Example this is feature count of CXCL2 gene in different samples CXCL2 1 0 0 0 0 0 0 ...
written 9 months ago by Genomics20

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