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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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
[COLOR="Red"][I][B]Error[/B][/I][/COLOR] [B]Can't read file: output.bw[/B]
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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