User: oriolebaltimore

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Posts by oriolebaltimore

<prev • 41 results • page 1 of 5 • next >
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Answer: A: Given a bed file with range of peaks, is it possible to identify the summit of t
... Thanks Jared. I just found another solution by Pierre. However, that just gives the coverage at the summit but not the position of that summit on chromosome. https://www.biostars.org/p/7726/ ...
written 17 days ago by oriolebaltimore110
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Given a bed file with range of peaks, is it possible to identify the summit of the peak
... Hello, Given a bed file with ranges of peaks and corresponding BAM file, can we identify the apex of each peak. Example: bed file: chr1 100 175 chr1 220 235 For first peak 'chr1 100-175' the apex of the peak could be at chr 1 140. Given the BAM file and bed file, can I get the p ...
rna-seq written 17 days ago by oriolebaltimore110 • updated 17 days ago by Alex Reynolds28k
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Comment: A: Can we combine adjacent peaks in ATAC-Seq fata
... Thanks Charles for your suggestion. ...
written 17 days ago by oriolebaltimore110
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Answer: A: Can we combine adjacent peaks in ATAC-Seq fata
... After I posted the original question, I read NucleoATAC paper by Schep AN et al. In nucleoATAC, one of the step includes extending identifying region by "bedtools slop". I extended for 200bp. I get good results now. Following are links posted previously which I missed. https://www.biostars.org/p ...
written 20 days ago by oriolebaltimore110
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Comment: A: Can we combine adjacent peaks in ATAC-Seq fata
... Thanks Friederike. For example, I see two different peaks in a 5kb Gene. A peak near 5'UTR and first exon and another peak near exon 7. I am not sure if chromatin is open only at these two sites. For same samples, I see RNA expression is very high in test sample compared to control. I was wonderi ...
written 28 days ago by oriolebaltimore110
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Can we combine adjacent peaks in ATAC-Seq fata
... Hi I just started to analyze ATAC-Seq data. I am not an expert and trying uderstand with data from NCBI and I am working on it. I did not come across anywhere, about how to deal with peaks next to each other such as adjacent peaks with at least a gap of 100 bases. In such case, is it okay to combi ...
sequencing written 29 days ago by oriolebaltimore110
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GSVA for mouse scRNA-Seq
... Dear Group, Is there a workflow for single sample enrichment analysis using either ssGSEA or GSVA for scRNA-Seq data from mouse. I am interested in running enrichment analysis on every cell from a mouse (mm.edb ). Thanks Adrian. ...
scrna-seq gsva written 9 weeks ago by oriolebaltimore110
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Answer: A: htseq-counts output merge into one matrix ??
... Is it considered best practice to sum up reads across replicates or to run HTSeq on merged BAM File after ccombing fastqs. Thanks Adrian ...
written 5 months ago by oriolebaltimore110
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When to remove duplicates using deduplication in Exome-Seq
... Hello group, To remove bias in calculating variant frequencies, we tend to remove PCR optical duplicates in Illumina exome-Seq protocols. However, in targeted sequencing, we do not remove PCR duplicates. I am not sure about Illumina truseq rapid exome sequencing library approach. Should the BAM ...
trueseq dna-seq exome-seq truseq gatk written 6 months ago by oriolebaltimore110 • updated 6 months ago by Charles Warden7.0k
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Comment: A: Bigwig format and operation
... I also responded to another similar post and requested the same question in the same forum. I apologize if that violates duplicate question rules. ...
written 7 months ago by oriolebaltimore110

Latest awards to oriolebaltimore

Popular Question 28 days ago, created a question with more than 1,000 views. For ssGSEA on RNA-Seq data from TCGA
Popular Question 9 weeks ago, created a question with more than 1,000 views. For ssGSEA on RNA-Seq data from TCGA
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Cuffmerge and cuffdiff on bam file generated by STAR alignment
Popular Question 5 months ago, created a question with more than 1,000 views. For ssGSEA on RNA-Seq data from TCGA
Popular Question 5 months ago, created a question with more than 1,000 views. For ssGSEA on RNA-Seq data from TCGA
Popular Question 9 months ago, created a question with more than 1,000 views. For ssGSEA on RNA-Seq data from TCGA
Popular Question 2.1 years ago, created a question with more than 1,000 views. For ssGSEA on RNA-Seq data from TCGA
Popular Question 2.1 years ago, created a question with more than 1,000 views. For RNA-Seq raw fastq files from TCGA

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