Harish harish0201
harish0201
/ convert_GTF_to_BED12.sh
Created
June 20, 2021 06:59
— forked from gireeshkbogu/convert_GTF_to_BED12.sh
How to convert GTF format into BED12 or BIGBED format?
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| # see below for UPDATES that include more shorter ways of conversions | |
| # How to convert GTF format into BED12 format (Human-hg19)? | |
| # How to convert GTF or BED format into BIGBED format? | |
| # Why BIGBED (If GTF or BED file is very large to upload in UCSC, you can use trackHubs. However trackHubs do not accept either of the formats. Therefore you would need bigBed format) | |
| # First, download UCSC scripts | |
| wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred | |
| wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredToBed | |
| wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed |