Mercurial > repos > padge > gtf_to_bed_script
comparison README.rst @ 0:ed0d0eda36a9 draft default tip
"planemo upload for repository https://github.com/usegalaxy-be/galaxytools/tree/main/gtf_to_bed commit 66fba7c9dccfddadce13aad591f441c66c3c309b-dirty"
| author | padge |
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| date | Wed, 29 Sep 2021 13:50:53 +0000 |
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| -1:000000000000 | 0:ed0d0eda36a9 |
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| 1 bwakit | |
| 2 ======= | |
| 3 | |
| 4 Written by Guy Bottu for the GenePattern server of VIB BioinforlmaticsCore, | |
| 5 takes as input a GTF file and writes a BED file in 12 column format | |
| 6 with information about transcripts, for use with RSeqC. | |
| 7 | |
| 8 The "thick" information is about the coding region, ideally it goes from | |
| 9 start codon to stop codon, but is information is lacking (e.g. because | |
| 10 of missing sequence or missing annotation), we use the CDS information. | |
| 11 For some transcripts there are multiple start or stop codons. We amways | |
| 12 choose the "thick" so that is has maximum length. | |
| 13 | |
| 14 If there is no CDS information (as for ncRNA) the "thick" will have just a | |
| 15 repeat of the transcript start position, as per BED convention. | |
| 16 | |
| 17 modified for integration under GenePattern | |
| 18 | |
| 19 usage : perl gtf_to_bed.pl <GTF file> <output file> |