Data from: Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence

Oppold A, Schmidt H, Rose M, Hellman SL, Dolze F, Ripp F, Weich B, Schmidt-Ott U, Schmidt E, Kofler R, Hankeln T, Pfenninger M

Date Published: March 20, 2017

DOI: http://dx.doi.org/10.5061/dryad.c8h50

 

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Title find-uniq-BLAST-hits.pl
Downloaded 3 times
Description This script filters duplicates from a BLAST table (-outfmt 6). When the identical data (in our case Pool-Seq reads) is blasted against similar reference sequences (in our case variants of a specific transposable element,i.e. the Cla-element), identical query sequences might fit to multiple reference sequences. This produces duplicates in the merged BLAST output. With this script retains the first occurrence of a query sequence and outputs a table of the same format as the input (BLAST -outfmt 6).
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Title PosinExons.py
Downloaded 3 times
Description Annotation of genomic locations that fall into exons.
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Title PosinGenes.py
Downloaded 8 times
Description Annotation of genomic locations that fall into genes (including introns).
Download PosinGenes.py (1.683 Kb)
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Title MF_50Mio_pe.sorted.bam
Downloaded 3 times
Description 50 Mio random pe reads of Pool-Seq data MF (Rhone-Alpes) mapped to Crip Laufer draft genome
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Title MG_50Mio_pe.sorted.bam
Downloaded 4 times
Description 50 Mio random pe reads of Pool-Seq data MG (Hessen, Germany) mapped to Crip_Laufer draft genome. Raw reads available at EMBL-EBI ENA ERS1590059
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Title NMF_50Mio_pe.sorted.bam
Downloaded 3 times
Description 50 Mio random pe reads of Pool-Seq data NMF (Lorraine) mapped to Crip_Laufer draft genome. Raw reads available at EMBL-EBI ENA ERS1590060
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Title SI_50Mio_pe.sorted.bam
Downloaded 4 times
Description 50 Mio random pe reads of Pool-Seq data SI (Piemont, Italy) mapped to Crip_Laufer draft genome. Raw reads available at EMBL-EBI ENA ERS1590061
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Title SS_50Mio_pe.sorted.bam
Downloaded 2 times
Description 50 Mio random pe reads of Pool-Seq data MG (Andalusia, Spain) mapped to Crip_Laufer draft genome. Raw reads available at EMBL-EBI ENA ERS1590062
Download SS_50Mio_pe.sorted.bam.gz (3.481 Gb)
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When using this data, please cite the original publication:

Oppold A, Schmidt H, Rose M, Hellman SL, Dolze F, Ripp F, Weich B, Schmidt-Ott U, Schmidt E, Kofler R, Hankeln T, Pfenninger M (2017) Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence. Molecular Ecology 26(12): 3256–3275. http://dx.doi.org/10.1111/mec.14111

Additionally, please cite the Dryad data package:

Oppold A, Schmidt H, Rose M, Hellman SL, Dolze F, Ripp F, Weich B, Schmidt-Ott U, Schmidt E, Kofler R, Hankeln T, Pfenninger M (2017) Data from: Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.c8h50
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