Datasets

Data were generated with the BEERS simulator.

Two genomes were simulated at each of three levels of complexity.

Approximately 40% of reads involve introns. The fragment length distribution has minimum length equal to 100 bases, mean equal to 200 bases and maximum length equal to 500 bases.

Genomes and Annotation

The annotation files contain the gene models and the levels at which each gene is expressed. The files with stem "geneinfo" contain the gene models, both bed and gtf formats are provided. The files with stem "featurequantifications" have the expression levels, given as counts. The genome sequence for P.falciparum is also included.

Download:
human.tar.bz2 (human.tar.bz2.md5sum)
File name File size in mb
simulator_config_featurequantifications_hg19 32.7
simulator_config_geneinfo_hg19_BED 7.2
simulator_config_geneinfo_hg19_GTF 39.1
malaria.tar.bz2 (malaria.tar.bz2.md5sum)
File name File size in mb
genome_sequence_pfal.fa 22.7
simulator_config_featurequantifications_pfal 1.5
simulator_config_geneinfo_pfal_GTF 1.4
simulator_config_geneinfo_pfal_BED.bed 0.4

Provided for each data set below is a .cig file which has the ground truth alignment information.

Dataset Test 1 (T1)

Download:
human_t1r1.tar.bz2 (human_t1r1.tar.bz2.md5sum)
File name File size in bytes
human_t1r1.tar.bz2 2244960190
simulated_reads_HG19t1r1.cig 3347201101
simulated_reads_HG19t1r1.forward.fa 1148888897
simulated_reads_HG19t1r1.reverse.fa 1148888897
simulated_reads_junctions-crossed_HG19t1r1.txt 107703771
simulated_reads2genes_HG19t1r1.txt 237173197
fraglenhisto_HG19t1r1.txt 3681
simulated_reads_HG19t1r1.log 631
human_t1r2.tar.bz2 (human_t1r2.tar.bz2.md5sum)
File name File size in bytes
human_t1r2.tar.bz2 1650963342
simulated_reads_HG19t1r2.cig 3347107018
simulated_reads_HG19t1r2.forward.fa 1148888897
simulated_reads_HG19t1r2.reverse.fa 1148888897
simulated_reads_junctions-crossed_HG19t1r2.txt 107605017
simulated_reads2genes_HG19t1r2.txt 237173703
fraglenhisto_HG19t1r2.txt 3619
simulated_reads_HG19t1r2.log 631
human_t1r3.tar.bz2 (human_t1r3.tar.bz2.md5sum)
File name File size in bytes
human_t1r3.tar.bz2 1651059886
simulated_reads_HG19t1r3.cig 3347307168
simulated_reads_HG19t1r3.forward.fa 1148888897
simulated_reads_HG19t1r3.reverse.fa 1148888897
simulated_reads_junctions-crossed_HG19t1r3.txt 107689281
simulated_reads2genes_HG19t1r3.txt 2371747983
fraglenhisto_HG19t1r3.txt 3617
simulated_reads_HG19t1r3.log 631
malaria_t1r1.tar.bz2 (malaria_t1r1.tar.bz2.md5sum)
File name File size in bytes
malaria_t1r1.tar.bz2 1485295032
simulated_reads_PFALt1r1.cig 3153103485
simulated_reads_PFALt1r1.forward.fa 1148888897
simulated_reads_PFALt1r1.reverse.fa 1148888897
simulated_reads_junctions-crossed_PFALt1r1.txt 31779635
simulated_reads2genes_PFALt1r1.txt 217475121
fraglenhisto_PFALt1r1.txt 3628
simulated_reads_PFALt1r1.log 626
malaria_t1r2.tar.bz2 (malaria_t1r2.tar.bz2.md5sum)
File name File size in bytes
malaria_t1r2.tar.bz2 1485141823
simulated_reads_PFALt1r2.cig 3152728883
simulated_reads_PFALt1r2.forward.fa 1148888897
simulated_reads_PFALt1r2.reverse.fa 1148888897
simulated_reads_junctions-crossed_PFALt1r2.txt 31759595
simulated_reads2genes_PFALt1r2.txt 217477424
fraglenhisto_PFALt1r2.txt 3631
simulated_reads_PFALt1r2.log 626
malaria_t1r3.tar.bz2 (malaria_t1r3.tar.bz2.md5sum)
File name File size in bytes
malaria_t1r3.tar.bz2 1485381027
simulated_reads_PFALt1r3.cig 3153134095
simulated_reads_PFALt1r3.forward.fa 1148888897
simulated_reads_PFALt1r3.reverse.fa 1148888897
simulated_reads_junctions-crossed_PFALt1r3.txt 31669723
simulated_reads2genes_PFALt1r3.txt 217475772
fraglenhisto_PFALt1r3.txt 3629
simulated_reads_PFALt1r3.log 626

Dataset Test 2 (T2)

Download:
human_t2r1.tar.bz2 (human_t2r1.tar.bz2.md5sum)
File name File size in bytes
human_t2r1.tar.bz2 1662841426
simulated_reads_HG19t2r1.cig 3365405132
simulated_reads_HG19t2r1.forward.fa 1148888897
simulated_reads_HG19t2r1.reverse.fa 1148888897
simulated_reads_junctions-crossed_HG19t2r1.txt 107831874
simulated_reads2genes_HG19t2r1.txt 237173474
fraglenhisto_HG19t2r1.txt 3614
simulated_reads_HG19t2r1.log 629
human_t2r2.tar.bz2 (human_t2r2.tar.bz2.md5sum)
File name File size in bytes
human_t2r2.tar.bz2 1662808903
simulated_reads_HG19t2r2.cig 3365465525
simulated_reads_HG19t2r2.forward.fa 1148888897
simulated_reads_HG19t2r2.reverse.fa 1148888897
simulated_reads_junctions-crossed_HG19t2r2.txt 107730289
simulated_reads2genes_HG19t2r2.txt 237175232
fraglenhisto_HG19t2r2.txt 3618
simulated_reads_HG19t2r2.log 629
human_t2r3.tar.bz2 (human_t2r3.tar.bz2.md5sum)
File name File size in bytes
human_t2r3.tar.bz2 1662653329
simulated_reads_HG19t2r3.cig 3365269694
simulated_reads_HG19t2r3.forward.fa 1148888897
simulated_reads_HG19t2r3.reverse.fa 1148888897
simulated_reads_junctions-crossed_HG19t2r3.txt 107672015
simulated_reads2genes_HG19t2r3.txt 237172228
fraglenhisto_HG19t2r3.txt 3620
simulated_reads_HG19t2r3.log 629
malaria_t2r1.tar.bz2 (malaria_t2r1.tar.bz2.md5sum)
File name File size in bytes
malaria_t2r1.tar.bz2 1512085790
simulated_reads_PFALt2r1.cig 3187657088
simulated_reads_PFALt2r1.forward.fa 1148888897
simulated_reads_PFALt2r1.reverse.fa 1148888897
simulated_reads_junctions-crossed_PFALt2r1.txt 31666380
simulated_reads2genes_PFALt2r1.txt 217475247
fraglenhisto_PFALt2r1.txt 3633
simulated_reads_PFALt2r1.log 624
malaria_t2r2.tar.bz2 (malaria_t2r2.tar.bz2.md5sum)
File name File size in bytes
malaria_t2r2.tar.bz2 1512096595
simulated_reads_PFALt2r2.cig 3187489618
simulated_reads_PFALt2r2.forward.fa 1148888897
simulated_reads_PFALt2r2.reverse.fa 1148888897
simulated_reads_junctions-crossed_PFALt2r2.txt217478092
simulated_reads2genes_PFALt2r2.txt 217477424
fraglenhisto_PFALt2r2.txt 3629
simulated_reads_PFALt2r2.log 624
malaria_t2r3.tar.bz2 (malaria_t2r3.tar.bz2.md5sum)
File name File size in bytes
malaria_t2r3.tar.bz2 1512245819
simulated_reads_PFALt2r3.cig 3188093676
simulated_reads_PFALt2r3.forward.fa 1148888897
simulated_reads_PFALt2r3.reverse.fa 1148888897
simulated_reads_junctions-crossed_PFALt2r3.txt 31716313
simulated_reads2genes_PFALt2r3.txt 217477767
fraglenhisto_PFALt2r3.txt 3630
simulated_reads_PFALt2r3.log 624

Dataset Test 3 (T3)

Download:
human_t3r1.tar.bz2 (human_t3r1.tar.bz2.md5sum)
File name File size in bytes
human_t3r1.tar.bz2 1686860897
simulated_reads_HG19t3r1.cig 3400829902
simulated_reads_HG19t3r1.forward.fa 1148888897
simulated_reads_HG19t3r1.reverse.fa 1148888897
simulated_reads_junctions-crossed_HG19t3r1.txt 107678983
simulated_reads2genes_HG19t3r1.txt 237177214
fraglenhisto_HG19t3r1.txt 3616
simulated_reads_HG19t3r1.log 630
human_t3r2.tar.bz2 (human_t3r2.tar.bz2.md5sum)
File name File size in bytes
human_t3r2.tar.bz2 1686570054
simulated_reads_HG19t3r2.cig 3400732532
simulated_reads_HG19t3r2.forward.fa 1148888897
simulated_reads_HG19t3r2.reverse.fa 1148888897
simulated_reads_junctions-crossed_HG19t3r2.txt 107715629
simulated_reads2genes_HG19t3r2.txt 237172284
fraglenhisto_HG19t3r2.txt 3620
simulated_reads_HG19t3r2.log 630
human_t3r3.tar.bz2 (human_t3r3.tar.bz2.md5sum)
File name File size in bytes
human_t3r3.tar.bz2 1686583257
simulated_reads_HG19t3r3.cig 3401027682
simulated_reads_HG19t3r3.forward.fa 1148888897
simulated_reads_HG19t3r3.reverse.fa 1148888897
simulated_reads_junctions-crossed_HG19t3r3.txt 107557541
simulated_reads2genes_HG19t3r3.txt 237171581
fraglenhisto_HG19t3r3.txt 3618
simulated_reads_HG19t3r3.log 630
malaria_t3r1.tar.bz2 (malaria_t3r1.tar.bz2.md5sum)
File name File size in bytes
malaria_t3r1.tar.bz2 1574460571
simulated_reads_PFALt3r1.cig 3257236138
simulated_reads_PFALt3r1.forward.fa 1148888897
simulated_reads_PFALt3r1.reverse.fa 1148888897
simulated_reads_junctions-crossed_PFALt3r1.txt 31826887
simulated_reads2genes_PFALt3r1.txt 217479021
fraglenhisto_PFALt3r1.txt 3630
simulated_reads_PFALt3r1.log 625
malaria_t3r2.tar.bz2 (malaria_t3r2.tar.bz2.md5sum)
File name File size in bytes
malaria_t3r2.tar.bz2 1574838459
simulated_reads_PFALt3r2.cig 3258428938
simulated_reads_PFALt3r2.forward.fa 1148888897
simulated_reads_PFALt3r2.reverse.fa 1148888897
simulated_reads_junctions-crossed_PFALt3r2.txt31756360
simulated_reads2genes_PFALt3r2.txt 217474114
fraglenhisto_PFALt3r2.txt 3630
simulated_reads_PFALt3r2.log 625
malaria_t3r3.tar.bz2 (malaria_t3r3.tar.bz2.md5sum)
File name File size in bytes
malaria_t3r3.tar.bz2 1574541266
simulated_reads_PFALt3r3.cig 3257469557
simulated_reads_PFALt3r3.forward.fa 1148888897
simulated_reads_PFALt3r3.reverse.fa 1148888897
simulated_reads_junctions-crossed_PFALt3r3.txt31716397
simulated_reads2genes_PFALt3r3.txt 217475274
fraglenhisto_PFALt3r3.txt 3630
simulated_reads_PFALt3r3.log 625