Hello Everyone,
I am using DEXSeq to find out differential usage of exons.
I want to know about the usage of gene aggregation option. After reading DEXSeq tutorial, I could understand that if I provide -r yes, it would merge the genes which have overlapping exons. I do not want to do this, so I used -r no. However I could not find any diiference in output.
Below i am posting the command which I am using as well as the output:
command: python dexseq_prepare_annotation.py -r no hg19.ensemblfortophat.gtf output.gff
Output:
chr1 dexseq_prepare_annotation.py aggregate_gene 11869 14412 . + . gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 11869 11871 . + . transcripts "ENST00000456328"; exonic_part_number "001"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 11872 11873 . + . transcripts "ENST00000456328+ENST00000515242"; exonic_part_number "002"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 11874 12009 . + . transcripts "ENST00000456328+ENST00000515242+ENST00000518655"; exonic_part_number "003"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 12010 12057 . + . transcripts "ENST00000456328+ENST00000515242+ENST00000450305+ENST00000518655"; exonic_part_number "004"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 12058 12178 . + . transcripts "ENST00000456328+ENST00000515242+ENST00000518655"; exonic_part_number "005"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 12179 12227 . + . transcripts "ENST00000456328+ENST00000515242+ENST00000450305+ENST00000518655"; exonic_part_number "006"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 12595 12612 . + . transcripts "ENST00000518655"; exonic_part_number "007"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 12613 12697 . + . transcripts "ENST00000456328+ENST00000515242+ENST00000450305+ENST00000518655"; exonic_part_number "008"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 12698 12721 . + . transcripts "ENST00000456328+ENST00000515242+ENST00000518655"; exonic_part_number "009"; gene_id "ENSG00000223972"
Please let me know if used command is incorrect.
Thank you,
Regards,
Mudita
I am using DEXSeq to find out differential usage of exons.
I want to know about the usage of gene aggregation option. After reading DEXSeq tutorial, I could understand that if I provide -r yes, it would merge the genes which have overlapping exons. I do not want to do this, so I used -r no. However I could not find any diiference in output.
Below i am posting the command which I am using as well as the output:
command: python dexseq_prepare_annotation.py -r no hg19.ensemblfortophat.gtf output.gff
Output:
chr1 dexseq_prepare_annotation.py aggregate_gene 11869 14412 . + . gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 11869 11871 . + . transcripts "ENST00000456328"; exonic_part_number "001"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 11872 11873 . + . transcripts "ENST00000456328+ENST00000515242"; exonic_part_number "002"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 11874 12009 . + . transcripts "ENST00000456328+ENST00000515242+ENST00000518655"; exonic_part_number "003"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 12010 12057 . + . transcripts "ENST00000456328+ENST00000515242+ENST00000450305+ENST00000518655"; exonic_part_number "004"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 12058 12178 . + . transcripts "ENST00000456328+ENST00000515242+ENST00000518655"; exonic_part_number "005"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 12179 12227 . + . transcripts "ENST00000456328+ENST00000515242+ENST00000450305+ENST00000518655"; exonic_part_number "006"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 12595 12612 . + . transcripts "ENST00000518655"; exonic_part_number "007"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 12613 12697 . + . transcripts "ENST00000456328+ENST00000515242+ENST00000450305+ENST00000518655"; exonic_part_number "008"; gene_id "ENSG00000223972"
chr1 dexseq_prepare_annotation.py exonic_part 12698 12721 . + . transcripts "ENST00000456328+ENST00000515242+ENST00000518655"; exonic_part_number "009"; gene_id "ENSG00000223972"
Please let me know if used command is incorrect.
Thank you,
Regards,
Mudita
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