Dataset Open Access

Genomic DNA transposition induced by human PGBD5 (Accompanying Scripts for Computational Analyses)

Henaff, Elizabeth; Henssen, Anton; Mason, Christopher E.; Kentsis, Alex

Contact person(s)
Henaff, Elizabeth

We include the bash scripts, python code and command-line parameters used to prepare, map, and analyze NGS sequencing data generated from a modified version of flanking sequence exponential anchored (FLEA) PCR to identify genomic insertion locations of a transposable element reporter construct. In summary, we map these reads to a hybrid genome consisting in the human reference hg19 and the reporter plasmid, identify reads that span the insertion breakpoint and thus recover the genomic insertion loci. 

Please find more details in the supplied README. 

 

This collection of scripts corresponds to the data analysis in the following publication:

Genomic DNA transposition induced by human PGBD5

Anton Henssen, Elizabeth Henaff, Eileen Jiang, Amy Eisenberg, Julianne R. Carson, Camila Villasante, Mondira Ray, Eric Still, Melissa Burns, Jorge Gandara, Cedric Feschotte, Christopher E. Mason, Alex Kentsis

 

 

Files (14.3 kB)
Name Size
generate_lumpy_command.bam.out.readlen.sh md5:5a2cf316e14647fb39441a5ccb36f301 5.1 kB Download
generate_mem_map.r1.r2.mem.cpu.out.sample.FOR_PBNEO.sh md5:eabbb4420f01a86d842beb32e8f869e6 3.6 kB Download
lumpy_bed2non-red_bed.py md5:b39f13c06c2ba806dc7e89b18d98231a 1.2 kB Download
lumpy_vcf2genloci_bed.sh md5:0b6bf57a95e300f72b2e1e84dcaf81f4 468 Bytes Download
P7_adapter_list.txt md5:e18ab24c48f7e83176279ac385ce204d 419 Bytes Download
README.bin md5:00a57da82b13fecfc5024c5157ed2589 3.4 kB Download

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