User: Lila M

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Lila M 410
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410
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UK
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6 hours ago
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3 years, 3 months ago
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Posts by Lila M

<prev • 270 results • page 1 of 27 • next >
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How to deal with wig files separate bu watson and crick strand
... 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 ...
deeptools groseq wig tssprofile written 2 days ago by Lila M 410
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Comment: C: how to get correlation between the counts over each gene at the same timepoint (
... that's exactly what I want! thanks! ...
written 2 days ago by Lila M 410
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Comment: C: how to get correlation between the counts over each gene at the same timepoint (
... 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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Comment: C: how to get correlation between the counts over each gene at the same timepoint (
... 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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Comment: C: how to get correlation between the counts over each gene at the same timepoint (
... How do you know any other way to do that? ...
written 3 days ago by Lila M 410
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Comment: C: how to get correlation between the counts over each gene at the same timepoint (
... 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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how to get correlation between the counts over each gene at the same timepoint (two replicates)
... 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 ...
htseq correlation rna-seq replication written 3 days ago by Lila M 410 • updated 3 days ago by Nicolas Rosewick7.2k
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Comment: C: how can I get the coverage over introns only in a RNA-seq experiment?
... 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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how can I get the coverage over introns only in a RNA-seq experiment?
... 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 ...
introns coverage rna-seq written 10 weeks ago by Lila M 410
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Comment: C: Problems running VC GATK: SAM/BAM/CRAM file dedup.bam is malformed
... And how can I get this info? ...
written 3 months ago by Lila M 410

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