User: VicGB

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VicGB0
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Posts by VicGB

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Comment: C: Is there any way to merge intervals based on a minimum overlap?
... Thanks! I will give it a try and reply back as soon as possible about the results. ...
written 6 months ago by VicGB0
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Comment: A: Is there any way to merge intervals based on a minimum overlap?
... Thanks for the suggestions, but because I wrote the post rapidly, I didn't explain myself correctly as I gave incorrect details. I have used bedtools intersect with -f and -F 0.5 and -e, so if only one region is covered enough. The thing is, [A B], [B C] and [C D] accomplish this requisite, but not ...
written 7 months ago by VicGB0
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Is there any way to merge intervals based on a minimum overlap?
... I'm trying to find a way to merge a bed file like bedtools merge does but requiring a minimum overlap between intervals. To illustrate my idea, let's suppose we have 4 genomic regions: A, B, C and D. A and B accomplish a minimum overlap that I wish and so does C and D, but I don't want to merge {A B ...
bed merge written 7 months ago by VicGB0 • updated 7 months ago by Alex Reynolds28k
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Comment: C: Compare two datasets knowing that one of them must have quite more mapped reads
... Sorry. I only wanted to illustrate a case with RNA-Seq data, but my dataset is not RNA-Seq Sequencing. We use on the treated sample a endonuclease which recognize some elements on the genome that should be present on the untreated sample, and that's why I expect more mapped reads (and actually what ...
written 14 months ago by VicGB0
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Comment: C: Compare two datasets knowing that one of them must have quite more mapped reads
... Hi! This is not RNA-Seq. That example was only to illustrate the situation. ...
written 14 months ago by VicGB0
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Compare two datasets knowing that one of them must have quite more mapped reads
... Hi everyone, I'm working with datasets in which I know one of them should have more signal globally specially in genes and I'm struggling with their comparison as most tools assume number of mapped reads as a factor to normalize. For example, to illustrate what I mean, let's suppose you are block ...
normalization chip-seq sequencing written 14 months ago by VicGB0
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Comment: C: Random downsampling without replacement in bam files only in regions with covera
... So the objetive of my "cherry-picking (lol?)" I that I'm using a genome assembly pipeline that does 20 random subsamplings to down the coverage to 150x in every subsampling and then do the consensus to reconstruct the genome. The problem is that I have some samples where coverage is so huge in some ...
written 2.2 years ago by VicGB0
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Random downsampling without replacement in bam files only in regions with coverage>x
... So I have a bam file with a huge coverage in some regions and I want to subsample randomly only reads that cover that zones, without sampling reads that cover zones of low coverages. Is there any tool or something? Thanks! ...
reads bam coverage written 2.2 years ago by VicGB0

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