Consolidation output files
File | Description |
|---|---|
_Condensed_Raw.fasta | This file contains all the original reads that were used for the condensation. |
_Cycle#.fasta | A _cycle#.fasta file is created for each cycle of the condensation that is carried out, where # is the cycle number. This file contains the consensus reads that were produced by the condensation cycle. |
_OrgSampleID.txt | This file saves the original sample IDs so that NextGENe can reference them for further analysis, such as sequence alignment. |
_Parameters.txt | This file contains information about the settings that were used for the project. If condensation was carried out as a preliminary step and then alignment or assembly was carried out as part of the same project, then a _Parameters.txt file is created that contains the settings for all the project steps. |
_StatInfo.txt | This file provides various statistics about the condensation process. • The number of sequences that matched to indices • The number of condensed reads that was produced • The average condensed read length • The average coverage within each condensed read • The username for the user who ran the analysis if User Management is turned on |
_Uncondensed_Raw.fasta | This file contains all the reads that were not used for condensation. |
TempViewDir.giv | You can use this file to graphically view the Consolidation results in the NextGENe Condensation Results tool. See The NextGENe Condensation Results Filter Tool. Note: This file is created only if “View Condensation Results” is selected. |
When Consolidation is the selected condensation method, each consensus read is assigned a name that provides several key pieces of information about the read:
• Each name begins with the “>” character to indicate the beginning of the read name.
• A index number for the a 12 bp anchor sequence to which the sequence is matched.
• The 12 bp anchor sequence.
 | Reads that match to the reverse complement for the reference show do not show this 12 bp anchor sequence. Instead, the reverse complement sequence is shown. |
• A number that indicates the anchor sequence’s starting location in the consensus sequence.
• The left shoulder sequence.
• The right shoulder sequence.
• The number of forward reads that were used to generate the consensus sequence.
• The number of reverse reads that were used to generate the consensus sequence.
For example, consider a read named as shown below:
>67059_TCCTGACTCCAC_19_GACGGATG_CCACACCC_42_67< |
This read was generated from the 67059th index which contains the anchor sequence “TCCTGACTCCAC.” The anchor sequence begins at position 19 of the consensus read, with the sequence “GACGGATG” on its left and the sequence “CCACACCC” on its right. 42 forward and 67 reverse reads were used to generate the consensus sequence.