Automatic Tissuecut Anomaly After Editing Annotation File

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Introduction

The SAW (Spatial Annotation Workbench) tool is widely used for spatial annotation of genomic data. However, users may encounter issues with automatic tissuecut after editing the annotation file. In this article, we will discuss a case where a user encountered an automatic tissuecut anomaly after editing the annotation file and provide a solution to fix the issue.

Background

The user was using SAW v7.1 to rerun a stereo-seq data set after adding a new gene into the annotation gff3 file. The new gene was successfully detected, but the newly generated spatial cluster expanded across the tissue border and created unnecessary new clusters.

Edited Annotation File

The edited annotation file contained the following changes:

Chr06   GDB     five_prime_UTR  27990812        27990828        .       -       .       Parent=ZH06G26570.1;
Chr06   ming    gene    28022916        28023601        .       +       .       ID=ZH06G26580;Name=ZH06G26580;
Chr06   GDB     mRNA    28022916        28023601        .       +       .       ID=ZH06G26580.1;Parent=ZH06G26580;
Chr06   GDB     exon    28022916        28023601        .       +       .       Parent=ZH06G26580.1;
Chr06   GDB     five_prime_UTR  28022916        28022917        .       +       .       Parent=ZH06G26580.1;
Chr06   GDB     CDS     28022918        28023601        .       +       0       Parent=ZH06G26580.1;
Chr06   MSU_osa1r7      gene    28057644        28061546        .       +       .       ID=ZH06G26585;Name=ZH06G26585;Note=AP2%20domain%20containing%20protein%2C%20expressed
Chr06   MSU_osa1r7      mRNA    28057644        28061546        .       +       .       ID=ZH06G26585.1;Name=ZH06G26585.1;Parent=ZH06G26585
Chr06   MSU_osa1r7      exon    28057644        28057925        .       +       .       ID=ZH06G26585.1:exon_1;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      exon    28058074        28058365        .       +       .       ID=ZH06G26585.1:exon_2;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      exon    28058649        28058731        .       +       .       ID=ZH06G26585.1:exon_3;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      exon    28058998        28059097        .       +       .       ID=ZH06G26585.1:exon_4;Parent=ZH06G26585.1Chr06   MSU_osa1r7      exon    28059337        28059410        .       +       .       ID=ZH06G26585.1:exon_5;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      exon    28059642        28059692        .       +       .       ID=ZH06G26585.1:exon_6;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      exon    28060371        28060447        .       +       .       ID=ZH06G26585.1:exon_7;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      exon    28060553        28061546        .       +       .       ID=ZH06G26585.1:exon_8;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      five_prime_UTR  28057644        28057925        .       +       .       ID=ZH06G26585.1:utr_1;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      five_prime_UTR  28058074        28058365        .       +       .       ID=ZH06G26585.1:utr_2;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      five_prime_UTR  28058649        28058731        .       +       .       ID=ZH06G26585.1:utr_3;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      five_prime_UTR  28058998        28059097        .       +       .       ID=ZH06G26585.1:utr_4;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      five_prime_UTR  28059337        28059366        .       +       .       ID=ZH06G26585.1:utr_5;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      CDS     28059367        28059410        .       +       .       ID=ZH06G26585.1:cds_1;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      CDS     28059642        28059692        .       +       .       ID=ZH06G26585.1:cds_2;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      CDS     28060371        28060447        .       +       .       ID=ZH06G26585.1:cds_3;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      CDS     28060553        28061172        .       +       .       ID=ZH06G26585.1:cds_4;Parent=ZH06G26585.1
Chr06   MSU_osa1r7      three_prime_UTR 28061173        28061546        .       +       .       ID=ZH06G26585.1:utr_6;ParentZH06G26585.1
Chr06   ming    gene    28073998        28074434        .       +       .       ID=ZH06G26590;Name=ZH06G26590;
Chr06   GDB     mRNA    28073998        28074434        .       +       .       ID=ZH06G26590.1;Parent=ZH06G26590;
Chr06   GDB     exon    28073998        28074068        .       +       .       Parent=ZH06G26590.1;
Chr06   GDB     five_prime_UTR  28073998        28073998        .       +       .       Parent=ZH06G26590.1;
Chr06   GDB     CDS     28073999        28074068        .       +       0       Parent=ZH06G26590.1;
Chr06   GDB     exon    28074175        28074434        .       +       .       Parent=ZH06G26590.1;
Chr06   GDB     CDS     28074175        28074434        .       +       1       Parent=ZH06G26590.1;

Problem Description

The user encountered an automatic tissuecut anomaly after editing the annotation file. The newly generated spatial cluster expanded across the tissue border and created unnecessary new clusters.

Solution

To fix the automatic tissuecut anomaly, we need to modify the annotation file to ensure that the new gene is properly annotated and does not overlap with the existing genes.

Step 1: Review the Annotation File

Review the edited annotation file to ensure that the new gene is properly annotated and does not overlap with the existing genes.

Step 2: Modify the Annotation File

Modify the annotation file to ensure that the new gene is properly annotated and does not overlap with the existing genes. This may involve adding or removing features, such as exons, introns, or UTRs.

Step 3: Re-index the Annotation File

Re-index the annotation file to ensure that the new gene is properly indexed and does not overlap with the existing genes.

Step 4: Run the SAW Tool

Run the SAW tool to re-annotate the genomic data using the modified annotation file.

Conclusion

Q: What is the automatic tissuecut anomaly?

A: The automatic tissuecut anomaly is a problem that occurs when the SAW tool fails to properly annotate the genomic data after editing the annotation file. This can result in the newly generated spatial cluster expanding across the tissue border and creating unnecessary new clusters.

Q: What causes the automatic tissuecut anomaly?

A: The automatic tissuecut anomaly can be caused by a variety of factors, including:

  • Incorrect annotation: If the new gene is not properly annotated, it can cause the SAW tool to fail to properly annotate the genomic data.
  • Overlapping features: If the new gene overlaps with existing genes, it can cause the SAW tool to fail to properly annotate the genomic data.
  • Incorrect indexing: If the annotation file is not properly indexed, it can cause the SAW tool to fail to properly annotate the genomic data.

Q: How can I fix the automatic tissuecut anomaly?

A: To fix the automatic tissuecut anomaly, you can follow these steps:

  1. Review the annotation file: Review the edited annotation file to ensure that the new gene is properly annotated and does not overlap with the existing genes.
  2. Modify the annotation file: Modify the annotation file to ensure that the new gene is properly annotated and does not overlap with the existing genes. This may involve adding or removing features, such as exons, introns, or UTRs.
  3. Re-index the annotation file: Re-index the annotation file to ensure that the new gene is properly indexed and does not overlap with the existing genes.
  4. Run the SAW tool: Run the SAW tool to re-annotate the genomic data using the modified annotation file.

Q: What are some common mistakes that can cause the automatic tissuecut anomaly?

A: Some common mistakes that can cause the automatic tissuecut anomaly include:

  • Incorrect gene annotation: Failing to properly annotate the new gene can cause the SAW tool to fail to properly annotate the genomic data.
  • Overlapping gene features: Failing to properly annotate the new gene to avoid overlapping with existing genes can cause the SAW tool to fail to properly annotate the genomic data.
  • Incorrect indexing: Failing to properly index the annotation file can cause the SAW tool to fail to properly annotate the genomic data.

Q: How can I prevent the automatic tissuecut anomaly?

A: To prevent the automatic tissuecut anomaly, you can follow these best practices:

  • Carefully review the annotation file: Before editing the annotation file, carefully review it to ensure that the new gene is properly annotated and does not overlap with the existing genes.
  • Properly annotate the new gene: Ensure that the new gene is properly annotated and does not overlap with the existing genes.
  • Properly index the annotation file: Ensure that the annotation file is properly indexed to avoid any issues with the SAW tool.

Q: What resources are available to help me fix the automatic tissuecut anomaly?

A: There are several resources to help you fix the automatic tissuecut anomaly, including:

  • SAW documentation: The SAW documentation provides detailed information on how to use the SAW tool and troubleshoot common issues.
  • SAW community forum: The SAW community forum is a great place to ask questions and get help from other users who have experienced similar issues.
  • SAW support team: The SAW support team is available to provide technical support and help you troubleshoot any issues you may be experiencing.