Difference between revisions of "Preparing value data"
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You can create TDF files directly from BAM files or from wig files. | You can create TDF files directly from BAM files or from wig files. | ||
| − | == Creating TDF files == | + | == Creating TDF files (recommended)== |
* [[bam2tdf]]: convert read alignment to coverage plot | * [[bam2tdf]]: convert read alignment to coverage plot | ||
* [[wig2tdf]]: convert wig formatted data to tdf formatted data | * [[wig2tdf]]: convert wig formatted data to tdf formatted data | ||
| − | |||
== SAMTools pileup (includes diversity information, i.e. SNP track) == | == SAMTools pileup (includes diversity information, i.e. SNP track) == | ||
<em>Note: file name extension should contain .pileup</em> | <em>Note: file name extension should contain .pileup</em> | ||
The first step to be able to browse a pileup is to generate one from your BAM file. | The first step to be able to browse a pileup is to generate one from your BAM file. | ||
| − | + | ||
| − | samtools | + | samtools mpileup -f reference.fasta sorted.bam >sorted.pileup |
| − | + | ||
As you run this command, you'll see that the generated file can be huge, even for small BAM files. | As you run this command, you'll see that the generated file can be huge, even for small BAM files. | ||
To be able to browse it in GenomeView, it needs to be indexed with tabix, a tool that is also available from the SAMtools web page. | To be able to browse it in GenomeView, it needs to be indexed with tabix, a tool that is also available from the SAMtools web page. | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | + | sort -k1,1 -k2,2n sorted.pileup | bgzip -c > compressed.pileup.bgz | |
| + | tabix -s 1 -b 2 -e 2 compressed.pileup.bgz | ||
| + | |||
| + | |||
| + | ==Tab delimited pileup (extension should contain '.swig')== | ||
The file should be organized in four columns. | The file should be organized in four columns. | ||
The first column holds the identifier of the sequence, the second column contains the genomic position, the third column contains the number of reads on the forward strand, the final column contains the number of reads on the reverse strand. | The first column holds the identifier of the sequence, the second column contains the genomic position, the third column contains the number of reads on the forward strand, the final column contains the number of reads on the reverse strand. | ||
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Example: | Example: | ||
| − | + | chr1 11 46 43 | |
| − | chr1 11 46 43 | + | chr1 12 47 50 |
| − | chr1 12 47 50 | + | chr1 13 48 61 |
| − | chr1 13 48 61 | + | chr1 14 53 79 |
| − | chr1 14 53 79 | + | |
| − | |||
<em>Note that the white-space between the columns are tabs, one tab between each column</em>. | <em>Note that the white-space between the columns are tabs, one tab between each column</em>. | ||
Once you have such a file, you can again index it for faster access and shorter download times. | Once you have such a file, you can again index it for faster access and shorter download times. | ||
| − | + | ||
| − | sort -T . -k1,1 -k2,2n filename | bgzip -c > filename.bgz | + | sort -T . -k1,1 -k2,2n filename | bgzip -c > filename.bgz |
| − | tabix -s 1 -b 2 -e 2 filename.bgz | + | tabix -s 1 -b 2 -e 2 filename.bgz |
| − | + | ||
It is recommended that you convert this format to TDF with [[wig2tdf]]. | It is recommended that you convert this format to TDF with [[wig2tdf]]. | ||
| − | + | [http://sourceforge.net/projects/samtools/files/samtools/|Download samtools] | |
| − | + | [https://sourceforge.net/projects/samtools/files/tabix/|Download tabix] | |
Latest revision as of 19:41, 14 May 2014
There are three formats supported for value/continuous data. The TDF format is by far the most appropriate and the other formats should be considered legacy support.
TDF is a tiled binary data format which contains the value plot, as well as multiple resolution summaries which allows fast retrieval at any scale.
This format is an alternative to wig and the bigwig formats and is typically used for data that has a value per chromosomal position, like for example coverage data.
You can create TDF files directly from BAM files or from wig files.
Creating TDF files (recommended)
- bam2tdf: convert read alignment to coverage plot
- wig2tdf: convert wig formatted data to tdf formatted data
SAMTools pileup (includes diversity information, i.e. SNP track)
Note: file name extension should contain .pileup The first step to be able to browse a pileup is to generate one from your BAM file.
samtools mpileup -f reference.fasta sorted.bam >sorted.pileup
As you run this command, you'll see that the generated file can be huge, even for small BAM files.
To be able to browse it in GenomeView, it needs to be indexed with tabix, a tool that is also available from the SAMtools web page.
sort -k1,1 -k2,2n sorted.pileup | bgzip -c > compressed.pileup.bgz tabix -s 1 -b 2 -e 2 compressed.pileup.bgz
Tab delimited pileup (extension should contain '.swig')
The file should be organized in four columns. The first column holds the identifier of the sequence, the second column contains the genomic position, the third column contains the number of reads on the forward strand, the final column contains the number of reads on the reverse strand.
- Identifier
- Genomic position (one-based)
- # forward reads
- # reverse reads
Example:
chr1 11 46 43 chr1 12 47 50 chr1 13 48 61 chr1 14 53 79
Note that the white-space between the columns are tabs, one tab between each column.
Once you have such a file, you can again index it for faster access and shorter download times.
sort -T . -k1,1 -k2,2n filename | bgzip -c > filename.bgz tabix -s 1 -b 2 -e 2 filename.bgz
It is recommended that you convert this format to TDF with wig2tdf.