User: mickey_95

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mickey_9520
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Posts by mickey_95

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Comment: C: RNA-seq expression patterns
... This sounds very reasonable, thanks! I just discovered the degPatterns() function from the DEGreport package: It clusters genes according to their pattern throughout time; as input I used DE genes resulting from LRT in DESeq2 ...
written 1 day ago by mickey_9520
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Comment: C: RNA-seq expression patterns
... Wow, thanks for the super quick and helpful reply!! Yes, I have already generated heatmaps and there are distinct groups/patterns, but I was wondering if that is the best approach for this. I was not aware of LRT, so far I've only used the default Wald test in DESeq2. Thanks a lot for pointing this ...
written 1 day ago by mickey_9520
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RNA-seq expression patterns
... Hi, I have an time-course RNA-seq data set with 8 different time points. I am trying to find expression patterns in the data - clusters of genes that change in similar ways throughout the experimental conditions. I guess one option would be to do pair-wise comparisons in DESeq2 by specifying the c ...
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Finding overlaps between GRanges objects
... Hi, I have a list of ChIP-seq peak regions and I am curious about those peaks overlapping annotated promoter regions. Inspired by this tutorial http://cbdm-01.zdv.uni-mainz.de/~jibnsale/teaching/chip-seq_exercises.html#functional-annotation-of-chip-seq-peaks (more specifically, sections 5.3 and 5 ...
peak iranges promoter chip-seq granges written 16 days ago by mickey_9520 • updated 16 days ago by Jimbou800
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Comment: C: TSS metaprofile using Deeptools
... Here are the first lines of the gtf file: chr1 ensembl_havana gene 5588466 5606131 . + . gene_id "ENSMUSG00000025905"; gene_version "14"; gene_name "Oprk1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; chr1 ensembl_havana gene 6206197 6276648 . + . gene_id "ENSMUSG0000002590 ...
written 4 months ago by mickey_9520
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TSS metaprofile using Deeptools
... Hi, I am trying to use Deeptools' computeMatrix and plotHeatmap functions to create TSS-centered metaprofiles over all genes. Ultimately, I would like to apply some additional filters, e.g. protein-coding, non-overlapping TSSs, above a certain size. But for an initial trial, I decided to just filte ...
gtf deeptools computematrix metaprofile written 4 months ago by mickey_9520 • updated 3 months ago by zhuobaowen10
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Creating TxDB objects from different sources
... Hi! I have been trying to understand the confusing world of genome annotations with the goal of consistently using the same version throughout all analyses for one project. Initially I was using UCSC annotations by simply loading the corresponding library in R: library(TxDb.Mmusculus.UCSC.mm1 ...
genome annotation txdb biomart ensembl written 4 months ago by mickey_9520
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Comment: C: ATAC-seq coverage tracks using bamCoverage from Deeptools
... Ah, good to know. Thanks a lot! ...
written 5 months ago by mickey_9520
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Comment: C: ATAC-seq coverage tracks using bamCoverage from Deeptools
... Thanks a lot for your help! I will try this way of normalization then. I've also seen people downsample their BAM files to the read number of the lowest sample. What is your take on that? Speaking of normalization and varying library sizes, I have a rather general question: When pooling different s ...
written 5 months ago by mickey_9520
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ATAC-seq coverage tracks using bamCoverage from Deeptools
... Hello! I have recently started to use Deeptools for my ATAC-seq data analysis and would like to get some feedback on the conversion of the BAM files to bigwig coverage tracks. I am interested in looking at TSS metaprofiles using either all fragments or fragments of only certain sizes. **For an all ...
deeptools bigwig atac-seq bamcoverage written 5 months ago by mickey_9520

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