User: newbie

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newbie70
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Posts by newbie

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Comment: C: How to get the phastcons score for protein coding genes and lncRNAs?
... thanq. And I posted may doubt in support bioconductor also. I got the reply. Here it is https://support.bioconductor.org/p/129140/#129223 ...
written 14 days ago by newbie70
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Comment: C: How to get the phastcons score for protein coding genes and lncRNAs?
... I found an R package [GenomicScores][1] to extract the `phastcons` scores. In the tutorial of the `GenomicScore` I see that information can be exxtracted only by each chromosome location. But I would like to know, whether there is any way to get the `phastcons` score for all protein coding genes ...
written 16 days ago by newbie70
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Comment: C: How to get the phastcons score for protein coding genes and lncRNAs?
... For the newly found lncRNAs, yes I will do it myself using `phast`. But how do I get the `phastcons` score for gencode protein-coding genes and known lncRNAs? ...
written 17 days ago by newbie70
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How to get the phastcons score for protein coding genes and lncRNAs?
... Dear All, I'm interested in checking the conservation of lncRNAs and protein-coding genes from Gencode and similarly from my data I also have some newly assembled lncRNAs which are not found in gencode. I would like to make a plot like below: ![enter image description here][1] The above image is ...
genome conservation phastcons rna-seq written 17 days ago by newbie70 • updated 15 days ago by gayachit170
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Comment: C: How to check the mutual exclusiveness between two genes?
... thanks a lot for the reply and the clear explanation. So, if the p-value is less than 0.05 it is seen as they are mutually exclusive. Am I right? ...
written 26 days ago by newbie70
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How to check the mutual exclusiveness between two genes?
... I have a total of 4500 samples. Among them `GeneA` is mutated in 600 and `GeneB` is in 900. Mutations in both `GeneA` and `GeneB` are 90 Mutations in only `GeneA` and no mutation in `GeneB` are 550 Mutations in only `GeneB` and no mutation in `GeneA` are 810 I see some people use fishers test t ...
mutual exclusivity mutation statistics written 26 days ago by newbie70 • updated 26 days ago by russhh5.2k
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Comment: C: How to get read counts on transcript level using featurecounts?
... small question. I have the sorted.bam files from `Hisat2` alignment. Can I use those bams for `RSEM` to calculate transcript expression? ...
written 5 weeks ago by newbie70
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Comment: C: How to get read counts on transcript level using featurecounts?
... you mean I can't get transcript level read counts with featureCounts? ...
written 5 weeks ago by newbie70
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How to get read counts on transcript level using featurecounts?
... I have used `featureCounts` to get the read counts one a gene level with the following command: featureCounts -a gencode.gtf -F GTF -p -s 2 -T 8 -o sample.txt sample.sorted.bam I'm interested in extracting the counts on a transcript level. My data is paired end and reverse stranded. I'm a bit ...
featurecounts geneexpression rna-seq written 5 weeks ago by newbie70 • updated 5 weeks ago by Gordon Smyth1.5k
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Comment: C: Question about processed microarray data from ArrayExpress
... thanks a lot @ATpoint ...
written 5 weeks ago by newbie70

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