User: Lila M
Lila M • 380
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- 2 years, 9 months ago
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Posts by Lila M
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Hi everybody, I'm, trying to follow this [protocol][1] using my own files, but I'm a bit stuck because I don't know how they get the [bigwig files][2]. Apparently the "replication signals at each location were determined as a percentage of the sum of the six normalized tag density signals", but do ...
written 10 days ago by
Lila M • 380
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C: repli-seq analysis pipeline
... what do you mean? can you please be more specific? Thanks! ...
written 17 days ago by
Lila M • 380
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C: repli-seq analysis pipeline
... But is somehow normalised to the Input or independent of it? Thanks! ...
written 17 days ago by
Lila M • 380
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C: repli-seq analysis pipeline
... Thank you very much! One more thing, how is the normalization doing?
...
written 17 days ago by
Lila M • 380
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... Hi every body,
I have a final data set (that I get using repliscan) with ratios a different time point (ES, MS and LS) over the human genome. I would like to analyze the data to see if there are differences in the replication time points
chr start end ratio1 ratio2 ratio3 ratioMS ratioLS ...
written 22 days ago by
Lila M • 380
• updated
17 days ago by
pbpanigrahi • 170
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C: repli-seq analysis pipeline
... Hi! Did you find the way to analyze the data? Im in the same situation! ...
written 23 days ago by
Lila M • 380
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... Hi,
I'm stuck analyzing a data set of genes that corresponds to different timepoints. I used DESeq for this approach but in that case I have different condition :
data file
ID time
14h_S1.bam 14h
14h_S7.bam 14h
16h_S2.bam 16h
16h_S8.bam 16h
19h_S3.bam 19h
19h ...
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... Super quick! Thanks very much!! ...
written 6 months ago by
Lila M • 380
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... That exactly what I was looking for!
Thanks! ...
written 6 months ago by
Lila M • 380
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... I understand what you say. My concern is if there is an easy option to construct a GRange (ranges and strand) object using the complete Dmelanogaster genome, let's say something like that, in a fast way:
genes <- GRanges(seqnames=c("chr2L" , "chr2R" , "chr3L" , "chr3R" , "chr4" , "chrX ...
written 6 months ago by
Lila M • 380
Latest awards to Lila M
Popular Question
6 months ago,
created a question with more than 1,000 views.
For How to convert bedgraph to bigwig?
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6 months ago,
created a question with more than 1,000 views.
For Looking for a ClueGO (cytoscape) tutorial
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6 months ago,
created a question with more than 1,000 views.
For how to compare 2 fasta sequences with perl
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created a question with more than 1,000 views.
For should I merge fastq files for different lanes before do QC?
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6 months ago,
created a question with more than 1,000 views.
For How to annotate TTS or TES
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voted more than 100 times.
Popular Question
11 months ago,
created a question with more than 1,000 views.
For how to compare 2 fasta sequences with perl
Popular Question
11 months ago,
created a question with more than 1,000 views.
For How to convert bedgraph to bigwig?
Scholar
14 months ago,
created an answer that has been accepted.
For A: How to plot a heat map for the top 30 differentially expressed genes.
Centurion
16 months ago,
created 100 posts.
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16 months ago,
voted at least 25 times.
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