Examples

Sample Data

Alignments

• ERR089819.bam (2.6 GB)

  Whole genome sequencing data of C. elegans from the following study.

• HG00096.chrom20.bam (278 MB)

  Sequencing of the chromosome 20 from a H. sapiens sample from 1000 Genomes project. The header of the BAM file was changed in order to contain only chromosome 20. Original file can be found here.

• kidney.bam (386 MB) and liver.bam (412 MB)

  Human RNA-seq sequencing data from from the paper of Marioni JC et al

Annotations

• human.64.gtf

  Human genome annotations from Ensembl database (v. 64).

• transcripts.human.64.bed

  Human transcripts in BED format from Ensembl database (v. 64).

Multisample BAM QC

• gh2ax_chip_seq.zip

  Example dataset from an unpublished ChiP-seq experiment with 4 condtions, each having 3 replicates (12 sampels in total). The archive contains BAM QC results for each sample and input configurations (normal: input.txt, with marked conditions: input.with_groups.txt) for command line version of Multisample BAM QC.

Counts QC

• mouse_counts_ensembl.txt

  Mouse counts data from a study investigating effects of D-Glucosamine:

• GlcN_countsqc_input.txt

  Command line input configuration for the counts data above.

• kidney.counts and liver.counts

  Counts data from the paper by Marioni JC et al.

• marioini_countsqc_input.txt

  Command line input configuration for the counts data above.

Clustering

• hmeDIP.bam (988M)

  MeDIP-seq of human embryonic stem cells from the study of Stroud H et al.

• input.bam (1.8G)

  Input data of the same study

Sample Output

BAM QC

Analysis of the WG-seq data (HG00096.chrom20.bam): QualiMap HTML report.

Analysis of the WG-seq data (ERR089819.bam): QualiMap PDF report.

RNA-seq QC

Analysis of RNA-seq data (kidney.bam, human.64.gtf): QualiMap HTML report.

Multisample BAM QC

Multisample analysis of 12 gH2AX ChiP-seq alignments: Qualimap HTML report.

Multisample analysis of the same data with condition assigned for each sample: Qualimap HTML report.

Counts QC

Counts QC HTML reports computed from RNA-seq experiment analyzing influence of D-Glucosamine on mice. The analysis was performed for 6 samples in 2 conditions - GlcN positive and negative (mouse_counts_ensembl.txt):

• Global report
• Comparison of conditions
• Sample 01 (GlcN negative)
• Sample 02 (GlcN negative)
• Sample 03 (GlcN negative)
• Sample 04 (GlcN positive)
• Sample 05 (GlcN positive)
• Sample 06 (GlcN positive)

Counts QC HTML reports from human RNA-seq data from study by Marioni JC et al (kidney.counts, liver.counts):

• Global report
• Comparison of conditions
• Sample 01 (Kidney)
• Sample 02 (Liver)

Clustering

Analysis of MeDIP-seq data: QualiMap HTML report.