User: chemcehn

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chemcehn190
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Posts by chemcehn

<prev • 17 results • page 1 of 2 • next >
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Answer: A: list of enhacer for specific cell line
... Here is the list you are looking for: http://enhancer.binf.ku.dk/presets/ It's in hg19, so you will have to use liftOver to convecr hg19 to hg18. ...
written 5.6 years ago by chemcehn190
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[solved] PHANTOM enhancers download
... Hello, Could you please advise where to find the FANTOM's list of cell-type specific enhancers? At this site there is only one file for human, which means these are non cell-specific: http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Enhancers/ I want to get a similar list as in the link above, ...
annotation chip-seq rna-seq written 5.6 years ago by chemcehn190
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RSAT problem with matrix conversion
... Hello, I am trying to convert a matrix from MEME using Rsat, but can't get it recognized. I tried to use as input the MEME matrix in the format PSPM and PSSM, but Rsat does not recognize any of them. I was trying the matrix with and without the header line, changing the parameters of the output fo ...
sequence alignment chip-seq written 5.7 years ago by chemcehn190
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[solved] IGV browser: export feature coordinates to BED file does not work
... Hello, I need to export from IGV browser to a BED file a set of specific features.found by the browser. It does not work. Could you please tell me how to do this? Thanks ...
genome chip-seq igv motif sequencing written 5.7 years ago by chemcehn190 • updated 5.7 years ago by Biostar ♦♦ 20
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Comment: C: Scan a large genome for the ocurrence of a single sequence motif?
... Hi Fidel, Could you please tell which input and output matrix formats should be selected at RSAT? Thanks! ...
written 5.7 years ago by chemcehn190
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Comment: C: Get gene names from genomic coordinates
... As far as I remember, you can install any new genome to HOMER, and then annotate your BED file with putative regions using *annotatePeaks* ...
written 5.7 years ago by chemcehn190 • updated 10 months ago by RamRS30k
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Answer: A: Get gene names from genomic coordinates
... prepare files with your target regions and your bacterial genome in the BED format, and then apply intersectBed from Bedtools or annotatePeaks from HOMER ...
written 5.7 years ago by chemcehn190
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[solved] MEME-ChIP: How to get the percentage of input regions which contain the motif?
... I am using MEME-ChIP to discover novel motifs from ChIP-seq data. Great program! My question is how to get the number of input regions which contain a newly found motif. I believe this information is kept somewhere as an intermediate result. Do you know how to get it? Thanks! [solved] I found this ...
chip-seq meme alignment motif written 5.7 years ago by chemcehn190 • updated 5.7 years ago by Biostar ♦♦ 20
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Answer: A: Metaseq: Average ChIP-seq signal over promoters error
... Just try another program, e.g. HOMER, it is much simpler to use ...
written 5.7 years ago by chemcehn190
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lnkRNA gene names not recognized by DAVID
... Hello, I am trying to analyze lnkRNA results from RNA-seq. Uploading lnkRNA gene names into DAVID, but it does not recognize most of them. The gene names look like this: AC000068.5; AP001625.4. Any suggestions how to sort out the problem with DAVID, and also what else one can do with this type of ...
annotation david rna-seq go written 5.7 years ago by chemcehn190 • updated 5.7 years ago by EagleEye6.7k

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