Tweet
Hi,
Most of you may not have this issues when you work on human and rodent transcriptomes. I am working on dog transcriptome, where genome annotations are not as good.
I downloaded the GTF file from Illumina's iGenome (Ensembl_BROADD2). When I look at their chr IDs (1st field), there are 38 chromosomes, plus MT, Un, and X
http://tophat.cbcb.umd.edu/igenomes.html
I also got canine GTF file directly from Ensembl website, in addition to chr. 1 to 38 , MT, X, It seems that Un was broken down into many AAEX.. and JH... (e.g AAEX03023950.1, JH373254.1).
ftp://ftp.ensembl.org/pub/release-68...nis_familiaris
Is it better to use IGenome's gtf or the one from Ensembl where ChrUn has been broken down? I look at the canine reference genome fasta file (from UCSC), it also seems to have many chrUn_AAEX... and chrUn_JH....
Just want to get your opinion for this.
thank you.
Most of you may not have this issues when you work on human and rodent transcriptomes. I am working on dog transcriptome, where genome annotations are not as good.
I downloaded the GTF file from Illumina's iGenome (Ensembl_BROADD2). When I look at their chr IDs (1st field), there are 38 chromosomes, plus MT, Un, and X
http://tophat.cbcb.umd.edu/igenomes.html
I also got canine GTF file directly from Ensembl website, in addition to chr. 1 to 38 , MT, X, It seems that Un was broken down into many AAEX.. and JH... (e.g AAEX03023950.1, JH373254.1).
ftp://ftp.ensembl.org/pub/release-68...nis_familiaris
Is it better to use IGenome's gtf or the one from Ensembl where ChrUn has been broken down? I look at the canine reference genome fasta file (from UCSC), it also seems to have many chrUn_AAEX... and chrUn_JH....
Just want to get your opinion for this.
thank you.