User: Zee_S

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Zee_S0
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Posts by Zee_S

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Pearson correlation between chIP-seq replicates is very poor- am I doing somethi
... Hello Colin, Thanks a lot of your reply. I looked at the link you sent me.. thank you! It looks like the tool mentioned here for correlation is the deep tools multibamsummary tool followed by plot correlation tool. I am wandering if this tool normalizes the bam files for sequencing depth or library ...
written 12 hours ago by Zee_S0
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Pearson correlation between chIP-seq replicates is very poor- am I doing something wrong in the normalization?!
... Hello everyone! I have several chIP-seq samples and their respective inputs and I want to find the Pearson correlation between different chIp replicates. I have read many posts and documentation about using deeptools, bedtools etc..for this purpose but for some reason, my correlation values are w ...
pearson correlation chip-seq written 13 hours ago by Zee_S0 • updated 8 hours ago by jomo018300
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Comment: C: is it necessary to normalize between a Paired-End and Single-End library?
... Hello, Thank you for your reply! my RNA seq library is PE only. and the chIP seq library is SE. I want to look at the correlation between my expression data and protein occupancy data. I made bins of the genome and I want to use bedtools to compute coverage across bins for the read libraries. but ...
written 1 day ago by Zee_S0
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is it necessary to normalize between a Paired-End and Single-End library?
... Hello everyone! I would like to look at the correlation between an RNAseq dataset and a Chip-seq dataset. I m using a CPM score per bin method but I'm not sure how the two libararies need to be normalised to e/o first. the RNA seq library is PE. and the ChIP seq library is SE. how to go about it p ...
normalization chip-seq rna-seq written 1 day ago by Zee_S0
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Comment: C: Chromosome Position From Ucsc Genome Browser
... hello everyone! I was just wandering, supposing you want to use this file later with, for example bedtools, do the start positions need to be listed as 0 instead of 1? thanks! ...
written 2 days ago by Zee_S0
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Comment: C: How to annotate repeats?
... Thank you so much for your input! This is very helpful! ...
written 3 days ago by Zee_S0
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Comment: C: How to get the total genic and intergenic length of a chromosome?
... does genic length mean excluding introns? because for my analyses I need to take intron coordinates into account. in that case, do I have to extract intron coordinates and use these in the intergenic calculation? thanks for your help ...
written 6 days ago by Zee_S0
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Comment: C: How to get the total genic and intergenic length of a chromosome?
... gene equates to TSS to TES. exon coordinates are within these intervals in a separate gtf file that I didn't show here. ...
written 6 days ago by Zee_S0
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Comment: C: How to get the total genic and intergenic length of a chromosome?
... I am posting here a 10-line snapshot of my genes.bed: thank you for your help! gene 1666 2818 gene 4096 5114 gene 21496 28507 gene 40486 46470 gene 49036 54240 gene 73329 91655 gene 99448 122165 gene 133623 138575 gene 141258 149665 gene 151974 157575 I did ...
written 6 days ago by Zee_S0 • updated 6 days ago by genomax46k
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Comment: C: How to get the total genic and intergenic length of a chromosome?
... Hello genomax, Yes, I have the coordinates of annotated genes in a bed file. and I also have a sizes.genome file with the chromosomes sizes. ...
written 6 days ago by Zee_S0

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