User: mudithekanayake

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Posts by mudithekanayake

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Comment: C: How to remove lines/headers from a SAM file after combined from different lanes
... Error File 'testONE_peaks.narrowPeak' - Unrecognized format line 1 of file: 1 4491713 4491913 testONE_peak_1 37 . 2.86003 3.72580 1.66717 80 (note: chrom names are case sensitive, e.g.: correct: 'chr1', incorrect: 'Chr1', incorrect: '1') When I tried to visualize in UCSC Genome browser, I got ...
written 7 weeks ago by mudithekanayake0
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Comment: C: How to remove lines/headers from a SAM file after combined from different lanes
... These are first few lines. ...
written 7 weeks ago by mudithekanayake0
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Comment: C: How to remove lines/headers from a SAM file after combined from different lanes
... I think you are correct. I called peaks using that file and I did not get any errors. But when I tried to visualize it using UCSC Genome browser I got a error that it does not recognize the first line. So I thought may be that was the issue. My narrowPeak file looks like this. Do you have any sugges ...
written 7 weeks ago by mudithekanayake0
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Comment: C: How to remove lines/headers from a SAM file after combined from different lanes
... Actually I don't have much idea about that. I was told to do so. Yes, I used samtools merge. ...
written 7 weeks ago by mudithekanayake0
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How to remove lines/headers from a SAM file after combined from different lanes
... Hello, I'm trying to call peaks using MACS2. Now I have merged 4 SAM files from different lanes into one. But it contains extra lines because of the merge step. Is there any simple way to remove the unnecessary lines? First few lines of the data looks like this. I need to remove lines 24, 25, 26 (L ...
genome R chip-seq rna-seq written 7 weeks ago by mudithekanayake0
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Comment: C: How to visualize narrowPeak file after peak calling using MACS?
... Oh. Thank you very much. I'll try that. Changing the chromosome name and adding a track header will do the work right? ...
written 8 weeks ago by mudithekanayake0
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How to visualize narrowPeak file after peak calling using MACS?
... Hello, I have done peak calling for H3K27ac mark using MACS. Now I have narrowPeak file. Should I need to rearrange the file to be visualized using UCSC Genome browser? It was not working when I tried to do that using both UCSC Genome browser and IGV. Thank you. This is how narrowPeak file looks l ...
genome chip-seq rna-seq written 8 weeks ago by mudithekanayake0 • updated 8 weeks ago by colin.kern900
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How to decide the parameters and parameter values when running ChIP-seq Peak Calling for H3K27ac data in MACS?
... I have alignment data in SAM files from ChIP-seq analysis for H3K27ac mark. I need to call peaks using MACS2. But I'm having issues with selecting parameters and values of the parameters. I will be really grateful if someone can help me figuring out this issue. Thank you. Mudith ...
genome next-gen chip-seq rna-seq written 8 weeks ago by mudithekanayake0 • updated 8 weeks ago by mark.ziemann1.2k
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Comment: C: How to do a GO enrichment analysis for large amount of data using R
... Thank you very much. I'll check it out. ...
written 6 months ago by mudithekanayake0
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How to do a GO enrichment analysis for large amount of data using R
... Hello, Is there any way to do a GO enrichment analysis in http://geneontology.org/ for large amount of data without doing one at a time? I have following kind of data. gene 1 ENSG00000230594 ENSG00000171155 ENSG00000224089 ENSG00000230347 ENSG00000236446 ENSG0000018647 ...
gene R go written 6 months ago by mudithekanayake0 • updated 6 months ago by Benn7.9k

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