Timeline for ATAC-seq peak annotation and downstream analysis
Current License: CC BY-SA 4.0
10 events
| when toggle format | what | by | license | comment | |
|---|---|---|---|---|---|
| Nov 15, 2019 at 10:45 | comment | added | kcm | "You need to make sure that featureCounts is configured properly so that it only uses the first base from each read" , can i get a more programmatic insight to it ,for rna seq data i do run featurecounts on bam file and get reads. So how do i do it here any resources or examples it would be really helpful for me.. | |
| Nov 15, 2019 at 10:34 | comment | added | Ian Sudbery | We take the union peak set as I described above, and then run featureCounts with the files of tags and the union peaks this will give you raw read counts. You need to make sure that featureCounts is configured properly so that it only uses the first base from each read. | |
| Nov 15, 2019 at 5:31 | comment | added | kcm | "their ATAC-seq signal was divided by scaling factors representing a median of signal ratios over a complete set of high-confidence ATAC-seq peaks (calculated with the function estimateSizeFactorsForMatrix,from DESeq2 v.1.20.0, Love et al. 2014)". Now Im confused how it can be done in deseq2 as it requires count matrix for analysis ,after homer analysis i get tag count which are not like raw read counts. | |
| Nov 15, 2019 at 5:13 | comment | added | kcm | fro ATAC seq how do I get rlog values as i see only tag counts or normalized tag counts | |
| Nov 14, 2019 at 22:52 | comment | added | Ian Sudbery | we've successfully used rlog in the past. | |
| Nov 14, 2019 at 19:20 | comment | added | kcm | I have a doubt , so i do see in paper where they cluster these chip seq or atac seq data.So is it just the tag count data which can be used or it needs some kind of normalisation? just in case of rna seq i use rlog or vst data for clustering or PCA ,which i do get from deseq. | |
| Nov 14, 2019 at 15:04 | comment | added | Ian Sudbery | Not "wrong" as such, but you'll get more peaks from the samples that have more reads, which is a bias in the analysis. | |
| Nov 14, 2019 at 14:49 | vote | accept | kcm | ||
| Nov 14, 2019 at 14:49 | comment | added | kcm | since i have already done with the alignment part as you suggested this part "taking the same number of reads from each)," right now i can do but i want to have some preliminary result .So would it be wrong to merge peal files from similar condition and go ahead ? | |
| Nov 14, 2019 at 11:35 | history | answered | Ian Sudbery | CC BY-SA 4.0 |