User: xiaofeiwang198266

Reputation:
20
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New User
Location:
United States
Last seen:
1 year, 7 months ago
Joined:
4 years, 6 months ago
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Posts by xiaofeiwang198266

<prev • 20 results • page 1 of 2 • next >
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Comment: C: HOMER target sequence location
... I have the same concern, did you figure it out. I am trying to use "Finding Instance of Specific Motifs" http://homer.ucsd.edu/homer/ngs/peakMotifs.html, but the results do not like what I am expected. Because the number of peaks/targets is not same as the number "knownResults.txt". ...
written 19 months ago by xiaofeiwang19826620
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HOMER getDifferentialPeaksReplicates.pl (why negative tag count)
... Dear folks, Does anyone have experience using getDifferentialPeaksReplicates.pl in HOMER, which is new added to HOMER in this Feb. It uses R/Bioconductor and DESeq2 (by default) to perform the differential enrichment calculations. But, I don't know why I got negative tag count for my results? I pa ...
R next-gen chip-seq sequencing written 20 months ago by xiaofeiwang19826620
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Comment: C: Motif finding with HOMER
... answer the problem just for people who got same problem: Figure the problem out by installing weblogs and newer version of Ghostscript (9.10). ...
written 21 months ago by xiaofeiwang19826620
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Comment: C: Motif finding with HOMER
... Did you figure out your problems? I got same problem. (I used it many years ago, it worked well but now, I did not make it work. I see this "Sequence logos produced during motif finding are now rendered using SVG instead of relying on weblogo/ghostscript." http://homer.ucsd.edu/homer/. But, I did no ...
written 21 months ago by xiaofeiwang19826620
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Comment: C: Correlating ChIP-Seq peaks with isoform level expression
... H3K4me3 is associated with transcriptional activation. If there is enrichment for this histone mark, it is expected that the gene should be activated expressed. Am I right? ...
written 22 months ago by xiaofeiwang19826620
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Comment: C: Homer detailed annotation
... Also, I downloaded hg18 genome to see the difference with my custom genome. There are lots of information under ~/software/homer/data/genome/hg18: chrom.sizes hg18.rna hg18.tts hg18.tss hg18.stop hg18.splice5p hg18.splice3p hg18.miRNA hg18.aug hg18.repeats hg18.basic.annotation hg18.full.annotation ...
written 2.0 years ago by xiaofeiwang19826620
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Comment: C: Homer detailed annotation
... Sorghum bicolor. Does is matter for this? On my understanding, "loadGenome.pl" is to prepare a custom genome for use with HOMER, so I don't think it will pull any information from Homer? ...
written 2.0 years ago by xiaofeiwang19826620
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Comment: C: Homer detailed annotation
... I tired this but got this "Could not find full/detailed annotation file (~/software/homer/.//data/genomes/sorgBi1.31//sorgBi1.31.annotation)" I think I need this detailed annotation filed created when use loadGenome.pl, but don't know how or why it is not generated when using loadGenome.pl. ...
written 2.0 years ago by xiaofeiwang19826620
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Comment: C: Homer detailed annotation
... I will try and let people know. ...
written 2.0 years ago by xiaofeiwang19826620
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Comment: C: Homer detailed annotation
... Could I ask another question? It is about pos2bed.pl not associated with this one. Or, do I need to open another thread? ...
written 2.0 years ago by xiaofeiwang19826620

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