Compress/index input with bgzip+tabix
From PileLine
(Difference between revisions)
(Created page with 'GP files (both intervals and single position files) can be compressed+indexed with [http://samtools.sourceforge.net/tabix.shtml tabix]. PileLine now supports this format as input…') |
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== Compressing GP files with tabix == | == Compressing GP files with tabix == | ||
| - | # Download tabix software from: [http://samtools.sourceforge.net/tabix.shtml] | + | # Download tabix software from: [http://samtools.sourceforge.net/tabix.shtml http://samtools.sourceforge.net/tabix.shtml] |
| + | # Compress a file (for example a .bed) | ||
| + | cat myfile.bed | bgzip > myfile.bed.bgz | ||
| + | tabix -p bed myfile.bed.bgz | ||
| + | #tabix has now created the myfile.bed.bgz.tbi, which is the index. | ||
Revision as of 18:30, 15 April 2011
GP files (both intervals and single position files) can be compressed+indexed with tabix. PileLine now supports this format as input for its commands.
NOTE: PileLine will recognize a input file as compressed if they have the .bgz extension.
Compressing GP files with tabix
- Download tabix software from: http://samtools.sourceforge.net/tabix.shtml
- Compress a file (for example a .bed)
cat myfile.bed | bgzip > myfile.bed.bgz tabix -p bed myfile.bed.bgz #tabix has now created the myfile.bed.bgz.tbi, which is the index.
