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Complete list of next generation sequencing data analysis packages

Please find our current data analysis packages below. Should you have any questions or you're interested in some data analysis not listed below, please contact us.

Package I. Library quality, basis statistics

Library quality

ˇ Quality filtering of SOLiD SAGE tags for the selection the most reliable subset will be used in the further bioinformatics analysis.

ˇ Collecting SAGE library health information

- Chart: nucleotide distribution

- Chart: restriction site distribution

Basic statistics

ˇ SAGE library statistics

- Chart: Tag and count number distribution

SAGE library mapping (transcript database)

ˇ Mapping SAGE tags to a transcript database.

- Chart: Mapping position distribution

ˇ Filtering SAGE tags detected more times than defined threshold.

ˇ Filtering SAGE tags mapping to canonical (most 3') position.

ˇ Filtering SAGE tags mapping to non-canonical position.

ˇ Filtering SAGE tags mapping to a unique position in the reference database.

ˇ (Filtering SAGE tags mapping according to keyword.)(Transcript db dependent)

ˇ Collecting confidence information about the reliability of the mapping events.

Other

ˇ Collecting unobserved transcripts

ˇ Reference database statistics

Package II. Statistics, SAGE tag mapping to transcript database

Statistics: identification and mapping significants

ˇ Comparing pairs of SAGE tag libraries and performing statistical analysis for identifying tags with significant expression change.

- Chart: Count number scatter plot, significants > red

- Chart: Venn diagram

Mapping significant SAGE tags to transcript database.

- Chart: Count number scatter plot, significants >red

- Chart: Venn diagram

ˇ Filtering significant SAGE tags detected more times than defined threshold.

ˇ Filtering significant SAGE tags mapping to canonical (most 3') position.

ˇ Filtering significant SAGE tags mapping to non-canonical position.

ˇ Filtering significant SAGE tags mapping to a unique position in the reference database.

ˇ (Filtering SAGE tags mapping according to keyword.)(Transcript db dependent)

ˇ Collecting confidence information about the reliability of the mapping events.

Package III. - SAGE library mapping (genome)

Mapping SAGE tags to genome.

Chart: Chromosomal distribution

Chart: Intra-chromosomal distribution

BED file for genome browser visualization

ˇ Filtering SAGE tags detected more times than defined threshold.

ˇ Filtering SAGE tags mapping to a unique position in the reference database.

Mapping significant SAGE tags to genome.

- Chart: Chromosomal distribution

- Chart: Intra-chromosomal distribution

- BED file for genome browser visualization

ˇ Filtering significant SAGE tags detected more times then defined treshold.

ˇ Filtering significant SAGE tags mapping to a unique position in the reference database.

Package IV. - Antisense mapping

Mapping SAGE tags to the antisense strand of a transcript database.

- Chart: Sense-Antisense sibling tags (Count number)

- Chart: Sumarised Sense and Antisense (Count number)

ˇ Filtering antisense SAGE tags detected more times then defined treshold.

ˇ Filtering antisense SAGE tags according to mapping position.

ˇ Filtering antisense SAGE tags mapping to a unique position in the reference database.

ˇ (Filtering antisense SAGE tags mapping according toa keyword.)(Transcript db dependent)

Antisense mapping of significant tags

ˇ Comparing pairs of SAGE tag libraries and performing statistical analysis for identifying tags with significant antisense expression change.

ˇ Mapping significant SAGE tags to the antisense strand of a transcript database.

- Chart: Sense-Antisense CTDI

- Chart: Sense-Antisense normalized CTDI

- Chart: Sense-Antisense sibling tags (P value)

- Chart: Summarized Sense and Antisense P values of transcripts

ˇ Filtering significant antisense SAGE tags detected more times than defined threshold.

ˇ Filtering significant antisense SAGE tags according to mapping position.

ˇ Filtering significant antisense SAGE tags mapping to a unique position in the reference database.

ˇ (Filtering antisense SAGE tags mapping according to keyword.)(Transcript db dependent)

Package V. - comparing results to other experiments

ˇ Filtering tags mapped to a user defined set of transcripts (e.g. transcript lists from a parallel microarray experiments).

ˇ Filtering significant tags mapped to a user defined set of transcripts (e.g. transcript lists from other microarray experiments).

Should you have any questions or you're interested in some data analysis not listed below, please contact us.