gireeshkbogu
/ convert_GTF_to_BED12.sh
Last active
April 17, 2024 03:21
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 |
slowkow
/ hg19.rRNA.interval_list
Last active
April 9, 2023 14:56
Make a ribosomal RNA interval_list for Picard Tools CollectRnaSeqMetrics
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| @SQ SN:chrM LN:16571 | |
| @SQ SN:chr1 LN:249250621 | |
| @SQ SN:chr2 LN:243199373 | |
| @SQ SN:chr3 LN:198022430 | |
| @SQ SN:chr4 LN:191154276 | |
| @SQ SN:chr5 LN:180915260 | |
| @SQ SN:chr6 LN:171115067 | |
| @SQ SN:chr7 LN:159138663 | |
| @SQ SN:chr8 LN:146364022 | |
| @SQ SN:chr9 LN:141213431 |