User: Bioinfo_2006

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Bioinfo_200690
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Posts by Bioinfo_2006

<prev • 36 results • page 1 of 4 • next >
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Comment: C: Y-axes of Volcano plots
... Yes, the data does have pretty low values ...
written 16 days ago by Bioinfo_200690
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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 18 days ago by Bioinfo_200690 • updated 17 days ago by Buffo1.6k
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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 23 days ago by Bioinfo_200690 • updated 23 days ago by ATpoint21k
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Comment: C: ATAC-Seq trimming reads to 36bp
... ![almost 50-50][1] [1]: https://i.ibb.co/pbLmDLv/Capture.png ...
written 24 days ago by Bioinfo_200690
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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 24 days ago by Bioinfo_200690
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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 25 days ago by Bioinfo_200690
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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 25 days ago by Bioinfo_200690
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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 25 days ago by Bioinfo_200690
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Comment: C: ATAC-Seq trimming reads to 36bp
... I also checked for chrM using Samtools idxstats of the sorted bam file, and there are no MT reads present. ...
written 25 days ago by Bioinfo_200690
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Comment: C: ATAC-Seq trimming reads to 36bp
... Sequence length is between 25-75 after trimming for adapters because I had specified a minimum length of 25. The adapter is completely gone. Last time when I trimmed it to 36 bp, those flipped reads were gone. Am unable to figure out where it comes from. ...
written 25 days ago by Bioinfo_200690

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Popular Question 5.9 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 5.9 years ago, created a question with more than 1,000 views. For Calculating Expression Conservation Score Between Two Gene Co-Expression Networks

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