User: Lila M
Lila M • 410
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Posts by Lila M
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... Hi everybody,
I downloaded some wig files (GRO-seq data) that contains genomic read coverage (merging the two lanes of the same sample). Separate files were created for the Crick and Watson strands (sample1_strand-rep1_lane1.wig, sample1_strand+rep1_lane1.wig ,sample1_strand-rep1_lane2.wig, sample1 ...
written 2 days ago by
Lila M • 410
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... that's exactly what I want! thanks! ...
written 2 days ago by
Lila M • 410
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... Not exactly, because it gives to me the cor between replicates, and what I want to know is if the counts for the gene ENSG00000000003.14 is different in t1_S1 and t1_S2 (and also for the others genes) ...
written 3 days ago by
Lila M • 410
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... Maybe I miss explain what I want. I want to know the correlation for, lets say gene ENSG00000000003.14 in the two replicates, to see if there are differences in each replicate for each gene. I'm not interested in the correlation ENSG00000000003.14 and ENSG00000000005.5. Has more sense?
...
written 3 days ago by
Lila M • 410
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... How do you know any other way to do that? ...
written 3 days ago by
Lila M • 410
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... This is what I am doing, but as I have a huge number of genes, R gets stuck .
This is what I'm trying:
xx <- read.table(file="matrix_count", sep="\t", header = T)
cor(t(xx), method="pearson")
any other suggestion?
...
written 3 days ago by
Lila M • 410
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... Hi everybody,
I have the counts (obtained by HTSeq) for a lot of genes(~58,000) at different time points (replicates).
gene t1_S1 t1_S2
ENSG00000000003.14 0 0
ENSG00000000005.5 0 0
ENSG00000000419.12 ...
written 3 days ago by
Lila M • 410
• updated
3 days ago by
Nicolas Rosewick ♦ 7.2k
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... both , coverage plot and number of reads mapping to INTRONS will be nice :) ...
written 9 weeks ago by
Lila M • 410
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... Hi everybody,
I've just wondering the best way to get the coverage over introns (only) in RNA-seq experiments (human genome)
My first approach is to download the complete intron list from UCSC. Then I could get the overlaps (using bedtools intersect or samithing similar) with each bed file. Once I ...
written 10 weeks ago by
Lila M • 410
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... And how can I get this info? ...
written 3 months ago by
Lila M • 410
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