To begin with, I am wondering if this an 'issue' or 'by design'...
In cases where there are overlapping exons on the opposite strand, extract_exons.py merges overlapping exons, and consequently, skips exons that are on one of the strands. For example, see:
Here, the exons in the red boxes are skipped altogether in the output as shown below:
$ cat test.gtf
NC_000001.11 Gnomon gene 106046545 106048300 . + . gene_id "LOC105378886"; db_xref "GeneID:105378886"; gbkey "Gene"; gene "LOC105378886"; gene_biotype "lncRNA";
NC_000001.11 Gnomon exon 106046545 106046664 . + . gene_id "LOC105378886"; transcript_id "XR_001738171.1"; db_xref "GeneID:105378886"; gbkey "ncRNA"; gene "LOC105378886"; model_evidence "Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 3 samples with support for all annotated introns"; product "uncharacterized LOC105378886"; exon_number "1";
NC_000001.11 Gnomon exon 106047626 106047774 . + . gene_id "LOC105378886"; transcript_id "XR_001738171.1"; db_xref "GeneID:105378886"; gbkey "ncRNA"; gene "LOC105378886"; model_evidence "Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 3 samples with support for all annotated introns"; product "uncharacterized LOC105378886"; exon_number "2";
NC_000001.11 Gnomon exon 106048219 106048300 . + . gene_id "LOC105378886"; transcript_id "XR_001738171.1"; db_xref "GeneID:105378886"; gbkey "ncRNA"; gene "LOC105378886"; model_evidence "Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 3 samples with support for all annotated introns"; product "uncharacterized LOC105378886"; exon_number "3";
NC_000001.11 Gnomon gene 106047149 106073156 . - . gene_id "LOC105378885"; db_xref "GeneID:105378885"; gbkey "Gene"; gene "LOC105378885"; gene_biotype "lncRNA";
NC_000001.11 Gnomon exon 106072958 106073156 . - . gene_id "LOC105378885"; transcript_id "XR_947668.2"; db_xref "GeneID:105378885"; gbkey "ncRNA"; gene "LOC105378885"; model_evidence "Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 5 samples with support for all annotated introns"; product "uncharacterized LOC105378885, transcript variant X1"; exon_number "1";
NC_000001.11 Gnomon exon 106049083 106049196 . - . gene_id "LOC105378885"; transcript_id "XR_947668.2"; db_xref "GeneID:105378885"; gbkey "ncRNA"; gene "LOC105378885"; model_evidence "Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 5 samples with support for all annotated introns"; product "uncharacterized LOC105378885, transcript variant X1"; exon_number "2";
NC_000001.11 Gnomon exon 106047149 106048295 . - . gene_id "LOC105378885"; transcript_id "XR_947668.2"; db_xref "GeneID:105378885"; gbkey "ncRNA"; gene "LOC105378885"; model_evidence "Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 5 samples with support for all annotated introns"; product "uncharacterized LOC105378885, transcript variant X1"; exon_number "3";
NC_000001.11 Gnomon exon 106052487 106052524 . - . gene_id "LOC105378885"; transcript_id "XR_947670.2"; db_xref "GeneID:105378885"; gbkey "ncRNA"; gene "LOC105378885"; model_evidence "Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns"; product "uncharacterized LOC105378885, transcript variant X2"; exon_number "1";
NC_000001.11 Gnomon exon 106049083 106049196 . - . gene_id "LOC105378885"; transcript_id "XR_947670.2"; db_xref "GeneID:105378885"; gbkey "ncRNA"; gene "LOC105378885"; model_evidence "Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns"; product "uncharacterized LOC105378885, transcript variant X2"; exon_number "2";
NC_000001.11 Gnomon exon 106047149 106048295 . - . gene_id "LOC105378885"; transcript_id "XR_947670.2"; db_xref "GeneID:105378885"; gbkey "ncRNA"; gene "LOC105378885"; model_evidence "Supporting evidence includes similarity to: 100% coverage of the annotated genomic feature by RNAseq alignments, including 4 samples with support for all annotated introns"; product "uncharacterized LOC105378885, transcript variant X2"; exon_number "3";
$ cat test.gtf | extract_exons.py -
NC_000001.11 106046544 106046663 +
NC_000001.11 106047148 106048299 -
NC_000001.11 106049082 106049195 -
NC_000001.11 106052486 106052523 -
NC_000001.11 106072957 106073155 -
Does this have any effect on how the reads are mapped? Is there a consequence to not merging overlapping exons (either on the opposite strand or on the same strand)?
To begin with, I am wondering if this an 'issue' or 'by design'... In cases where there are overlapping exons on the opposite strand,
Here, the exons in the red boxes are skipped altogether in the output as shown below:
extract_exons.pymerges overlapping exons, and consequently, skips exons that are on one of the strands. For example, see:Does this have any effect on how the reads are mapped? Is there a consequence to not merging overlapping exons (either on the opposite strand or on the same strand)?