User: oriolebaltimore

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Posts by oriolebaltimore

<prev • 42 results • page 1 of 5 • next >
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Regressing on cell cycle genes in scRNA-Seq
... Dear group members, While analyzing single cell RNA-Seq data from early stage tumor and advanced stage tumors, is it recommended to normalize the cell cycle genes. If we regress the G1, G2M and S phase genes there are some downstream complications if one wants to find differences between quiescent ...
single-cell rna-seq written 11 months ago by oriolebaltimore160
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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 18 months ago by oriolebaltimore160
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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 18 months ago by oriolebaltimore160 • updated 18 months ago by Alex Reynolds31k
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Comment: A: Can we combine adjacent peaks in ATAC-Seq fata
... Thanks Charles for your suggestion. ...
written 18 months ago by oriolebaltimore160
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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 18 months ago by oriolebaltimore160
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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 19 months ago by oriolebaltimore160
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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 19 months ago by oriolebaltimore160 • updated 6 months ago by Biostar ♦♦ 20
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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 20 months ago by oriolebaltimore160
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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 23 months ago by oriolebaltimore160
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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 2.0 years ago by oriolebaltimore160 • updated 2.0 years ago by Charles Warden8.0k

Latest awards to oriolebaltimore

Popular Question 12 days ago, created a question with more than 1,000 views. For VarScan for tumor only files
Great Question 10 months ago, created a question with more than 5,000 views. For ssGSEA on RNA-Seq data from TCGA
Popular Question 10 months ago, created a question with more than 1,000 views. For Mutation calling rules in TCGA
Popular Question 10 months ago, created a question with more than 1,000 views. For VarScan for tumor only files
Great Question 18 months ago, created a question with more than 5,000 views. For ssGSEA on RNA-Seq data from TCGA
Popular Question 18 months ago, created a question with more than 1,000 views. For Mutation calling rules in TCGA
Popular Question 18 months ago, created a question with more than 1,000 views. For ssGSEA on RNA-Seq data from TCGA
Popular Question 18 months ago, created a question with more than 1,000 views. For filter BAM file for reads that map 100% identity
Popular Question 19 months ago, created a question with more than 1,000 views. For ssGSEA on RNA-Seq data from TCGA
Popular Question 20 months ago, created a question with more than 1,000 views. For ssGSEA on RNA-Seq data from TCGA
Popular Question 20 months ago, created a question with more than 1,000 views. For Cuffmerge and cuffdiff on bam file generated by STAR alignment
Popular Question 23 months ago, created a question with more than 1,000 views. For ssGSEA on RNA-Seq data from TCGA
Popular Question 23 months ago, created a question with more than 1,000 views. For ssGSEA on RNA-Seq data from TCGA
Popular Question 2.3 years ago, created a question with more than 1,000 views. For ssGSEA on RNA-Seq data from TCGA
Popular Question 3.6 years ago, created a question with more than 1,000 views. For ssGSEA on RNA-Seq data from TCGA
Popular Question 3.6 years ago, created a question with more than 1,000 views. For RNA-Seq raw fastq files from TCGA

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