Forum: Bioinformatics
02-14-2011, 12:30 AM
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Replies: 5
Views: 1,806
Long peaks
Hi
I've done a chip-seq experiment, and used the program MACS. When I look at the peaks in UCSC genome browser, the peaks are very long, see pdf file for example from mitochondrial chromosome. Is...
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Forum: Bioinformatics
02-07-2011, 02:58 AM
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Replies: 3
Views: 1,462
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Forum: Bioinformatics
02-07-2011, 12:48 AM
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Replies: 3
Views: 1,462
Missing strand _peaks.bed
Hi
I've tried to analyze my data with MACS, and want the file _peaks.bed that MACS gives. Does anyone know how to know which strand each peak is on? The file only contains
chrom start stop name...
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Forum: Bioinformatics
01-11-2011, 09:42 PM
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Replies: 1
Views: 6,621
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Forum: Bioinformatics
01-10-2011, 05:13 AM
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Replies: 1
Views: 2,343
MACS peaks.bed
Hi
I wounder how MACS score the peaks. When you run MACS you get a output peaks.bed, this file include chromosome, start, stop, peaknumber and a score. How does MACS create this score? Does the...
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Forum: Bioinformatics
12-22-2010, 02:28 AM
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Replies: 1
Views: 2,884
Human exon, intron and promotor bedfile
Hi
I have done a chip-seq analysis and got a file with name peaks.bed I want to investigate if the peaks are in the promotor, exon og intron of hg19. Does somebody know where to get the bedfiles of...
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Forum: Bioinformatics
12-21-2010, 09:47 PM
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Replies: 0
Views: 3,113
Exons from UCSC (Refseq)
Hi
I've tried to get bed files for human exon, intron and promotor region. Used the http://genome.ucsc.edu/ Table browser and choosed track RefSeq genes.
Then I use intersectbed to see how many of...
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Forum: Bioinformatics
12-19-2010, 09:37 AM
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Replies: 2
Views: 1,471
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Forum: Bioinformatics
12-17-2010, 05:26 AM
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Replies: 2
Views: 1,471
MACS SAMfiles
Hi
I've used MACS to find peaks in a SAM file, and I got a line in the peaks.bed file in SAM with negative start (-98) so I cannot upload the file in UCSC genome browser.
chrM -98 4052...
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Forum: Bioinformatics
12-16-2010, 04:22 AM
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Replies: 1
Views: 16,388
convert wig to bigwig
I've used MACS and got one wig file per chromosome. I want to make a bigwig file and used the manual on ucsc http://genome.ucsc.edu/goldenPath/help/bigWig.html.
1. Should I put the wig files...
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Forum: Bioinformatics
12-16-2010, 01:05 AM
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Replies: 11
Views: 4,349
Thanks
I think it's strange ; it doesn't...
Thanks
I think it's strange ; it doesn't seem like it is unique sequences.
The read length is 50 bp. Do you think I should have changed the other parameters then? I should use the parameters...
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Forum: Bioinformatics
12-16-2010, 12:52 AM
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Replies: 11
Views: 4,349
So the conclusion is to use this parameters: ...
So the conclusion is to use this parameters:
bowtie hg19 -q input.fastq -m 1 -S bowtie_out
but isn't this the same as
bowtie hg19 -q input.fastq -m 1 --best --strata --all -S bowtie_out if the m 1...
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Forum: Bioinformatics
12-16-2010, 12:33 AM
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Replies: 11
Views: 4,349
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Forum: Bioinformatics
12-16-2010, 12:12 AM
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Replies: 11
Views: 4,349
Bowtie parameters
I'm new in next generation sequencing, and I use Bowtie for the first time. Is there someone that know how to get only the sequences that only have one match? I tried this command.
bowtie hg19 -q...
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Forum: General
12-15-2010, 11:40 PM
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Replies: 1
Views: 2,226
Help with Bowtie, only unique alignments
I'm new in next generation sequencing, and I use Bowtie for the first time. Is there someone that know how to get only the sequences that only have one match? I tried this command.
bowtie hg19 -q...
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