The Position Navigator can be used to show all notable base positions in contigs, and to quickly navigate to them.

Press the button Position Navigator in the Task Entry overview, or choose it from the context menu. A selection dialog is opened where the targets that should be included in the position navigator can be chosen. By default, all failed targets and targets with warnings are selected, because only those can have problems that appear as positions of interest.

After the selection dialog has been confirmed, the targets are scanned for problems. This requires that the full data of a target is loaded.

After the scanning was performed, the Position Navigator window opens up, showing four different tabs: Summary, Targets with Failed Analysis, Homopolymer InDels, and Consensus Edits.

Summary

Shows a summary of the found problems. The links here can be used to jump to the corresponding section.

Targets with Failed Analysis

The table shows all targets that have warnings or failed the analysis checks. Only the most important reason of failure is listed per target.

When contigs are modified, the table is automatically updated. Resolved problem positions are not removed, but they are marked as solved. They can be removed with the Remove Solved button.

The following columns are shown in the table:

State

Can be (error), (warning), (solved).

Target

The affected target.

Position

The base position where the error occurs. Some errors (like wrong contig length) don't refer to a specific position.

Error Type

Shows the type of analysis check that has failed.

Homopolymer InDels

The table shows all insertions or deletions that are related to a homopolymer, a sequence of identical bases (at least 2 bases in reference sequence). This is a common problem for some next-gen sequencing data.

When contigs are modified, the table is automatically updated. Resolved problem positions are not removed, but they are marked as solved. They can be removed with the Remove Solved button.

The following columns are shown in the table:

State

Can be (problem), (solved problem).

Target

The affected target.

Position

The position that was determined as the error position of this homopolymer. This position is detected by analyzing the read alignment. In some cases this detection fails, and the real problem position may differ.

Length in Ref

The length of the homopolymer in the ref.-seq.. Only homopolymers with a length 2 or larger in the reference sequence are found.

The duplication hint means:

If we have an "CAAT" in the ref.-seq., and an "C-AT" in the contig => homopolymer (deletion)

If we have an "C-AT" in the ref.-seq., and an "CAAT" in the contig => No homopolymer, because ref.-seq. has only one A

Type

The type of the homopolymer can be Insertion or Deletion. Insertion means that an additional homopolymer base does not appear in the ref.-seq..

Base

The base that is repeated in the homopolymer.

Coverage

The number of aligned reads on the detected homopolymer error position.

Ref Match Abs.

The absolute number of aligned reads on the detected homopolymer error position that have the same base as the ref.-seq..

Ref Match Perc.

The number of aligned reads on the detected homopolymer error position that have the same base as the ref.-seq. as a percentage of the total coverage at this position.

The Auto-Correct button can be used to perform an auto-correction of the homopolymer indels, considering the ref.-seq. and the read alignment. This auto-correction can only be done for contigs that contain the reads as assembled reads. Targets without read have the value n/a. If a target has reads but still has the value n/a, no clear error position could be detected in the alignment. These homopolymer indels have to be checked manually.

When the auto-correct button is pressed, a dialog window appears where the requirements and thresholds can be defined, that must be reached by the detected homopolymer positions before they are processed.

Correct Insertions/Deletions

Allows to perform the auto-correction for insertions or deletions only. By default it will be performed for both.

Required minimum homopolymer length

Defines the minimum base count that the homopolymer must have in the ref.-seq..

Required absolute read coverage

Defines the minimum number of reads that must be aligned at the detected homopolymer error position.

Required percentage of coverage matching

Defines the minimum percent identity of the reads to the ref.-seq. base at the detected homopolymer error position.

Allow Single Strand Rating

This option takes into account that many of the homopolymer indels demonstrate a strand bias.

If this option is set, the absolute read coverage and the percentage of coverage matching must be reached either by the aligned forward reads or by the aligned reverse reads.

If it is not set, the sum of all reads (forward and reverse) at the detected homopolymer error position must reach the thresholds.

A preview on the bottom of the settings window shows the number of homopolymers that reach the currently set thresholds.

Consensus Edits

The table shows all edits (manual or automatic) that were performed in the targets. The following columns are shown in the table:

Targets

The affected target.

Position

The position that was edited.

Operation

The kind of edit that was performed.

Comment

A comment that was set for this edit.

Timestamp

The date and time when the edit was performed.