Fasta filtering and DNAm scoring pipeline
This file takes in maxee filtered and dereplicated sample fasta files. Samples are then checked for the correct sequence site “CCGGG” or “GGG” at the beginning of each sequence. Samples are trimmed to be the same length and dereplicated using USEARCH10. A database of each set of unique sequences of...
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Dryad Digital Repository
2018
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Online Access: | https://dx.doi.org/10.5061/dryad.n4h3672/3 https://datadryad.org/resource/doi:10.5061/dryad.n4h3672/3 |
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ftdatacite:10.5061/dryad.n4h3672/3 2023-05-15T16:17:22+02:00 Fasta filtering and DNAm scoring pipeline De Paoli-Iseppi, Ricardo Deagle, Bruce Polanowski, Andrea McMahon, Clive Dickinson, Joanne Hindell, Mark Jarman, Simon 2018 https://dx.doi.org/10.5061/dryad.n4h3672/3 https://datadryad.org/resource/doi:10.5061/dryad.n4h3672/3 unknown Dryad Digital Repository https://dx.doi.org/10.5061/dryad.n4h3672 http://creativecommons.org/publicdomain/zero/1.0 CC0 Age Birds DNA methylation Epigenetics DREAM Flinders Island Fisher Island Tasmania Ardenna tenuirostris dataset Dataset DataFile 2018 ftdatacite https://doi.org/10.5061/dryad.n4h3672/3 https://doi.org/10.5061/dryad.n4h3672 2021-11-05T12:55:41Z This file takes in maxee filtered and dereplicated sample fasta files. Samples are then checked for the correct sequence site “CCGGG” or “GGG” at the beginning of each sequence. Samples are trimmed to be the same length and dereplicated using USEARCH10. A database of each set of unique sequences of CCGGG or GGG starting sites is created e.g. a methylated and unmethylated database. Samples are compared against these two databases and counts recorded to generate scores between 0-1. DNAm scores can then be further filtered on read depth, standard deviation or output as needed. Dataset Fisher Island DataCite Metadata Store (German National Library of Science and Technology) Flinders ENVELOPE(-66.667,-66.667,-69.267,-69.267) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Age Birds DNA methylation Epigenetics DREAM Flinders Island Fisher Island Tasmania Ardenna tenuirostris |
spellingShingle |
Age Birds DNA methylation Epigenetics DREAM Flinders Island Fisher Island Tasmania Ardenna tenuirostris De Paoli-Iseppi, Ricardo Deagle, Bruce Polanowski, Andrea McMahon, Clive Dickinson, Joanne Hindell, Mark Jarman, Simon Fasta filtering and DNAm scoring pipeline |
topic_facet |
Age Birds DNA methylation Epigenetics DREAM Flinders Island Fisher Island Tasmania Ardenna tenuirostris |
description |
This file takes in maxee filtered and dereplicated sample fasta files. Samples are then checked for the correct sequence site “CCGGG” or “GGG” at the beginning of each sequence. Samples are trimmed to be the same length and dereplicated using USEARCH10. A database of each set of unique sequences of CCGGG or GGG starting sites is created e.g. a methylated and unmethylated database. Samples are compared against these two databases and counts recorded to generate scores between 0-1. DNAm scores can then be further filtered on read depth, standard deviation or output as needed. |
format |
Dataset |
author |
De Paoli-Iseppi, Ricardo Deagle, Bruce Polanowski, Andrea McMahon, Clive Dickinson, Joanne Hindell, Mark Jarman, Simon |
author_facet |
De Paoli-Iseppi, Ricardo Deagle, Bruce Polanowski, Andrea McMahon, Clive Dickinson, Joanne Hindell, Mark Jarman, Simon |
author_sort |
De Paoli-Iseppi, Ricardo |
title |
Fasta filtering and DNAm scoring pipeline |
title_short |
Fasta filtering and DNAm scoring pipeline |
title_full |
Fasta filtering and DNAm scoring pipeline |
title_fullStr |
Fasta filtering and DNAm scoring pipeline |
title_full_unstemmed |
Fasta filtering and DNAm scoring pipeline |
title_sort |
fasta filtering and dnam scoring pipeline |
publisher |
Dryad Digital Repository |
publishDate |
2018 |
url |
https://dx.doi.org/10.5061/dryad.n4h3672/3 https://datadryad.org/resource/doi:10.5061/dryad.n4h3672/3 |
long_lat |
ENVELOPE(-66.667,-66.667,-69.267,-69.267) |
geographic |
Flinders |
geographic_facet |
Flinders |
genre |
Fisher Island |
genre_facet |
Fisher Island |
op_relation |
https://dx.doi.org/10.5061/dryad.n4h3672 |
op_rights |
http://creativecommons.org/publicdomain/zero/1.0 |
op_rightsnorm |
CC0 |
op_doi |
https://doi.org/10.5061/dryad.n4h3672/3 https://doi.org/10.5061/dryad.n4h3672 |
_version_ |
1766003217090478080 |