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