DerTALEv2: Difference between revisions
(Created page with "DerTALEv2 filters predictions of TALE target boxes by the presence of differentially expressed regions in a defined vicinity around a predicted target box. As input, DerTALEv2 requires a list of target box predictions as generated by the PrediTALE tool, which is included in the DerTALEv2 JAR file. For determining differentially expressed regions, DerTALEv2 also needs mapped RNA-seq data after Xanthomonas infection (treatment) and control in BAM format, which is the sta...") |
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DerTALEv2 filters predictions of TALE target boxes by the presence of differentially expressed regions in a defined vicinity around a predicted target box. | '''DerTALEv2''' filters predictions of TALE target boxes by the presence of differentially expressed regions in a defined vicinity around a predicted target box. | ||
As input, DerTALEv2 requires a list of target box predictions as generated by the PrediTALE tool, which is included in the DerTALEv2 JAR file. | As input, DerTALEv2 requires a list of target box predictions as generated by the PrediTALE tool, which is included in the DerTALEv2 JAR file. | ||
For determining differentially expressed regions, DerTALEv2 also needs mapped RNA-seq data after Xanthomonas infection (treatment) and control in BAM format, which is the standard output format of most mappers, and may be generated from the SAM format using samtools. For each BAM file, DerTALEv2 also needs an index file with the same base name as the BAM file but additional extension ".bai" (as generated by samtools). | For determining differentially expressed regions, DerTALEv2 also needs mapped RNA-seq data after ''Xanthomonas'' infection (treatment) and control in BAM format, which is the standard output format of most mappers, and may be generated from the SAM format using samtools. For each BAM file, DerTALEv2 also needs an index file with the same base name as the BAM file but additional extension ".bai" (as generated by samtools). | ||
Further parameters that can be specified include the number of predictions in the list that are considered (counting from top), the width of the region in which differential expression is considered, the width of the window that needs to be differentially expressed, and a threshold on the log (base 2) differential abundance (e.g., 1 for a two-fold induction). | Further parameters that can be specified include the number of predictions in the list that are considered (counting from top), the width of the region in which differential expression is considered, the width of the window that needs to be differentially expressed, and a threshold on the log (base 2) differential abundance (e.g., 1 for a two-fold induction). | ||
Revision as of 21:55, 24 May 2024
DerTALEv2 filters predictions of TALE target boxes by the presence of differentially expressed regions in a defined vicinity around a predicted target box.
As input, DerTALEv2 requires a list of target box predictions as generated by the PrediTALE tool, which is included in the DerTALEv2 JAR file.
For determining differentially expressed regions, DerTALEv2 also needs mapped RNA-seq data after Xanthomonas infection (treatment) and control in BAM format, which is the standard output format of most mappers, and may be generated from the SAM format using samtools. For each BAM file, DerTALEv2 also needs an index file with the same base name as the BAM file but additional extension ".bai" (as generated by samtools).
Further parameters that can be specified include the number of predictions in the list that are considered (counting from top), the width of the region in which differential expression is considered, the width of the window that needs to be differentially expressed, and a threshold on the log (base 2) differential abundance (e.g., 1 for a two-fold induction).
