User: Bioinfo_2006

gravatar for Bioinfo_2006
Bioinfo_2006130
Reputation:
130
Status:
Trusted
Location:
Last seen:
5 months, 1 week ago
Joined:
6 years, 11 months ago
Email:
r************@gmail.com

about me

Posts by Bioinfo_2006

<prev • 38 results • page 1 of 4 • next >
0
votes
2
answers
657
views
2
answers
Comment: C: Convert Granges list of peaks into consensus counts
... I edited the above now. Try it again. Once you read in all the peaks in your folder, use lapply to get the Granges which is stored as myPeaks. Then convert them to a list (myGRangesList). ...
written 6 months ago by Bioinfo_2006130
3
votes
2
answers
657
views
2
answers
Answer: A: Convert Granges list of peaks into consensus counts
... Hope someone finds this useful when they come across the ATAC-Seq tutorial peaks <- dir("ATAC_Data/ATAC_Peaks_forCounting/", pattern = "*.narrowPeak", full.names = TRUE) myPeaks <- lapply(peaks, ChIPQC:::GetGRanges, simple = TRUE) myGRangesList<-GRangesList(myPeaks) ...
written 6 months ago by Bioinfo_2006130
0
votes
1
answer
308
views
1
answers
Comment: C: Y-axes of Volcano plots
... Yes, the data does have pretty low values ...
written 7 months ago by Bioinfo_2006130
1
vote
1
answer
308
views
1
answer
Y-axes of Volcano plots
... I have a DESeq2 object and generating a volcano plot of up, down and non-sig genes par(mar=c(5,5,5,5), cex=1.0, cex.main=1.4, cex.axis=1.4, cex.lab=1.4) topT <- as.data.frame(deseq2object) with(topT, plot(log2FoldChange, -log10(padj), pch=20, main="Volcano plot", cex=1.0, xlab=bquote ...
R enhancedvolcano volcanoplots written 7 months ago by Bioinfo_2006130 • updated 7 months ago by Buffo1.8k
6
votes
2
answers
657
views
5 follow
2
answers
Convert Granges list of peaks into consensus counts
... After ATAC-Seq analysis, I have a list of peaks ![Granges list of peaks][1] Now, I would like to merge our open regions from all samples into a set of non-redundant (no overlapping regions) open regions present in any sample (see example below). ![Identify non-reundant peaks][2] I tried the f ...
R bioconductor granges written 8 months ago by Bioinfo_2006130
0
votes
2
answers
521
views
2
answers
Comment: C: ATAC-Seq trimming reads to 36bp
... ![almost 50-50][1] [1]: https://i.ibb.co/pbLmDLv/Capture.png ...
written 8 months ago by Bioinfo_2006130
0
votes
2
answers
521
views
2
answers
Answer: C: ATAC-Seq trimming reads to 36bp
... Adding --nocontain option as mapping parameter in Bowtie2 solves the problem (without trimming the reads), however I have an equal percentage of multi-mappers, and unique ones. Would that be an issue? ...
written 8 months ago by Bioinfo_2006130
0
votes
2
answers
521
views
2
answers
Comment: C: ATAC-Seq trimming reads to 36bp
... the alignment rate is between 97-99% using untrimmed reads, and 100% in terms of trimmed reads ...
written 8 months ago by Bioinfo_2006130
0
votes
2
answers
521
views
2
answers
Comment: C: ATAC-Seq trimming reads to 36bp
... I see that the adapter is completely gone, no overrep sequences, and everything else in fastqc is a green. Was just going through the ENCODE pipeline where they trim the reads to 30 bp and this discussion at https://www.biostars.org/p/215988/ https://www.encodeproject.org/pipelines/ENCPL035XIO/ ...
written 8 months ago by Bioinfo_2006130
0
votes
2
answers
521
views
2
answers
Comment: C: ATAC-Seq trimming reads to 36bp
... Am going to pull out those reads, and also going to check mapping parameters for bowtie2. As Igor mentioned, the fragments could be shorter than the read length, and hence I see the flip whereas once I trim to 36bp I no longer see it. ...
written 8 months ago by Bioinfo_2006130

Latest awards to Bioinfo_2006

Popular Question 6.5 years ago, created a question with more than 1,000 views. For Finding Differentially Expressed Genes Across Multiple Cell Types In A Datset
Popular Question 6.5 years ago, created a question with more than 1,000 views. For Calculating Expression Conservation Score Between Two Gene Co-Expression Networks

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1648 users visited in the last hour