User: Hamilton

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Hamilton260
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7 years, 4 months ago
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7 years, 10 months ago
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Posts by Hamilton

<prev • 25 results • page 1 of 3 • next >
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How To Generate A Wiggle Output On Macs 2.0
... On MACS2.0, it seems there is no option for output wiggle file unlike previous versions with -S, --wig -w. is there any way to generate a wiggle output from ./macs2? THanks. ...
macs chip-seq written 7.4 years ago by Hamilton260 • updated 7.4 years ago by Ian5.5k
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How To Upload Repeat Mask Fasta File On Igv (Integrative Genomics Viewer)
... Using IGV, I am trying to upload repeat mask fasta file with extension .out or .align as well as identified peaks of chipseq TF data to see whether detected peaks are called in repeated mask regions or not. When i tried, IGV does not allow to upload repeat mask file of fasta format. do you know ho ...
chip-seq repeatmasker written 7.4 years ago by Hamilton260 • updated 6.3 years ago by marcosmorgan90
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Phastcons .Data To Binary Wig File
... I have chr.data phastcons scores for mm9 from UCSC genome browser. Btw i need corresponding binary wiggle files for them. chr.data has already fixed step wiggle format when i open up the file. But since extension is .data document format, tools which run with a wiggle file do not recognize it as a b ...
wiggle written 7.4 years ago by Hamilton260 • updated 6.0 years ago by Jorge Amigo11k
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Comment: C: Cisgenome Browser With Bar Files Vs Igv With Wig Files
... let me try to make it clear. -- the main question was whether i need any preprocessing procedures in conversion step from bam files to bar files for cisgenome or not. This is chipseq data of TF. ...
written 7.4 years ago by Hamilton260
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Cisgenome Browser With Bar Files Vs Igv With Wig Files
... I am looking at the interesting peaks on cisgenome browser with bar files(i generated them from bam file using converting functions in cisgnome such as barTobed). The other one, I uploaded wig files generated from MACS on IGV viewer. They are coming from the identical sample and i am comparing on ...
genome chip-seq written 7.5 years ago by Hamilton260 • updated 7.4 years ago by Ying W3.9k
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A General Evaluation Of Chipseq Data
... is there any measure to validate if the one chipseq experiment is good or not?? that is, the data are good enough to analyze or the second experiment should be redone as the 1st experiment was not good? how can we measure such a quality usually? sort of quality measure to account for non-redundant r ...
quality chip-seq written 7.5 years ago by Hamilton260 • updated 4.4 years ago by Biostar ♦♦ 20
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Time To Upload A Bigwig File With Around 12.55 Gb
... I am uploading a big wig file generated from MACS peak caller, the file size is 12.55 GB. It is running now. btw, I wonder if it will be eventually uploaded or not as it is a huge size. IGV is run with even such a huge wig file. how about ucsc genome browser? This is a mac computer with processor 2 ...
genome wiggle written 7.5 years ago by Hamilton260 • updated 7.5 years ago by David Langenberger9.0k
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How To Keep Up The Genome Browser Session Continuously
... Hi Folks, I generated a genome browser session with my chip-seq data for a specific chr region with high significant peak score. btw i would like to keep this session. The file does not work after for a while (probably after a few of days) how can i keep such a genome browser session as a file? ...
genome chip-seq ucsc written 7.5 years ago by Hamilton260 • updated 7.5 years ago by Sven0
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Comment: C: Chipseq Fastq Files
... any suggestions?? ...
written 7.6 years ago by Hamilton260
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Comment: C: Chipseq Fastq Files
... if i run with bowtie --phred64-quals -5 6 -3 6 -S: Error: reads file does not look like a FASTQ file ...
written 7.6 years ago by Hamilton260

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