3268394
doi
10.5281/zenodo.3268394
oai:zenodo.org:3268394
Hampus Olin
Molecular Evolution, Department of Cell and Molecular Biology, Uppsala University, 75124 Sweden.
Caitlin Vigetun Haughey
Molecular Evolution, Department of Cell and Molecular Biology, Uppsala University, 75124 Sweden.
Lisa Klasson
Molecular Evolution, Department of Cell and Molecular Biology, Uppsala University, 75124 Sweden.
Jacques Dainat
IMBIM - Department of Medical Biochemistry and Microbiology, Box 582, S-751 23 Uppsala, Sweden; National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, Uppsala Biomedicinska Centrum (BMC), Husargatan 3, S-751 23 Uppsala, Sweden.
GUESSmyLT: Software to guess the RNA-Seq library type of paired and single end read files
Erik Berner Wik
Molecular Evolution, Department of Cell and Molecular Biology, Uppsala University, 75124 Sweden.
info:eu-repo/semantics/openAccess
GNU General Public License v3.0 only
https://www.gnu.org/licenses/gpl-3.0-standalone.html
RNA-seq library paired single read
library
reads
<p>The choice of RNA-Seq library type defines the read orientation of the sequencing and the order in which the strands of cDNA are sequenced, which means that RNA-Seq reads from different library types can differ significantly. The information regarding library type can be very useful for reads to be assembled into a transcriptome or mapped to a reference assembly. This is because the library type can help to discern where in the transcriptome shorter ambiguous reads belong by using the read’s relative orientation and from which strand it was sequenced. Unfortunately, this information regarding the library type used is not included in sequencing output files and may be lost before the assembly of the data. Even when working with RNA-Seq data from public repositories there is no guarantee that the library type information is correct or that it exists at all. This is what GUESSmyLT aims to fix by looking at how reads map to a reference and together with gene annotation guess which library was used to generate the data.</p>
Software to guess the RNA-Seq library type of paired and single end read files using mapping and gene annotation.
Zenodo
2019-07-04
info:eu-repo/semantics/other
3268393
v1.0
1579936894.816615
30354316
md5:ec380e982f96166c2a2d5cfad8289e12
https://zenodo.org/records/3268394/files/GUESSmyLT-1.0.zip
public
10.5281/zenodo.3268393
isVersionOf
doi