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Hi,
Can anyone tell me how to convert SAM/BAM format to wiggle format?
Regards,
Pinki
Can anyone tell me how to convert SAM/BAM format to wiggle format?
Regards,
Pinki
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You could try the rsem-bam2wig utility from RSEM(http://deweylab.biostat.wisc.edu/rsem/docs.html). -
If you are doing ChIP-seq, MACS writes you wig files as part of its output and is really simple to use. Some other software chip-seq software packages do the same.--------------
EthanComment
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You can use bedtools to get a bedgraph:
samtools sort sample.bam sample.sorted
genomeCoverageBed -bg -ibam sample.sorted.bam -g chromsizes.txt > sample.bedgraph
#on second look, dawe already said this, but the page was down for me.Comment
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Yet another way if you have a raw SAM file:
TopHat has an undocumented tool, Wiggles, which will compute coverage of a SAM file and produce a bedgraph file (usage will tell you that it outputs a .wig file, but it really is a bedgraph file).
Note that the Wiggles tool will probably be removed from the source of TopHat as it is no longer used by the TopHat pipeline.Comment
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Hello Friends,
Thank you for your valuable information.Comment
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HiI tried using RSEM and I get segmentation fault. I tried using sorted bam file but still I get segmentation fault. Any clue on this? Thanks.Comment
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I also tried using bedtools as mentioned above.
Take a look here, examples 2 and 3.
But the output sample.bw is not a human readable file. But I have ot tried uploading them into ucsc yet. Why is it so? Anyone has tried above steps? Thanks.Code:Example 3 Summary: A slightly different way (than ex. 2) to create BigWig files from BAM Contributor: Assaf Gordon Date: 09-July-2010 Tools used: samtools, genomeCoverageBed, bedGraphToBigWig More Information : http://cancan.cshl.edu/labmembers/gordon/files/viz2.pdf ============================================================ Workflow: # 1. Convert SAM to BAM samtools view -S -b -o sample.bam sample.sam # 2. Sort the BAM file samtools sort sample.bam sample.sorted # 3. Create BedGraph coverage file genomeCoverageBed -bg -ibam sample.sorted.bam -g chromsizes.txt > sample.bedgraph # 4. Convert the BedGraph file to BigWig bedGraphToBigWig sample.bedgraph chromsizes.txt sample.bw
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bigwig is a binary format. UCSC has utilities for reading the file format, bigWigSummary bigWigToBedGraph etc.Originally posted by seq_GA View PostComment
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Originally posted by adamdeluca View Post
Thanks for your response. I tried uploading into ucsc but i get the following error:
I have uploaded the zipped test output.Code:[COLOR="Red"][I][B]Error[/B][/I][/COLOR] [B]Can't read file: output.bw[/B]
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bigWig files are to be linked from your ftp/http server. That way you don't need to transfer the whole file to UCSC, just what is needed for a given view. I don't think you can upload them to ucsc. bigWigInfo can parse the file you uploaded so it appears valid. You should be able to upload the bedGraph file from step 3.
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Hi adamdeluca,
Thanks for your response. I have a bedgraph as below:
Is there any procedure to upload them into tracks. Because I want to see the density graph like. Thanks.Code:chr10 68271 68272 44 chr10 68272 68274 43 chr10 68274 68275 46 chr10 68275 68282 50 chr10 68282 68283 52 chr10 68283 68284 55 chr10 68284 68285 54 chr10 68285 68287 59 chr10 68287 68289 62 chr10 68289 68291 54
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shouldn't you go for normalized reads visualization instead of raw reads(SAM/BAM) ?Comment
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Surprisingly to find that this problem is still not well resolved.Originally posted by pinki999 View Post
I write a python program "bam2wig.py" that is specially designed for RNA-seq, so it works fine for spliced read, for both single-end and pair-end, for both strand-specific and non-strand specific RNA-seq data.
The input BAM file should be sorted and indexed using SamTools before hand.
Best,Comment
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