Hi all.
I'm trying to map paired end illumina reads to a reference genome with a GFF3 file for annotation info. I compiled the genome sequence from separate files of each linkage groups plus the scaffolds which couldn't be assigned to linkage groups.
But running tophat2 like so:
ends up giving me this error:
I thought that maybe the names were off but it all looks like it matches.
and my GFF3 file looks like so:
Any suggestions here as to what I'm doing wrong would be most appreciated.
I'm trying to map paired end illumina reads to a reference genome with a GFF3 file for annotation info. I compiled the genome sequence from separate files of each linkage groups plus the scaffolds which couldn't be assigned to linkage groups.
But running tophat2 like so:
Code:
tophat -p 8 -G ~/path/to/annotation.gff3 index_name CAA_l1_1.fq.gz CAA_l1_2.fq.gz
Code:
[2013-11-21 12:19:21] Building transcriptome data files.. [2013-11-21 12:19:24] Building Bowtie index from annotation.fa [FAILED] Error: Couldn't build bowtie index with err = 1
Code:
bowtie2-inspect -n gi|339751252|ref|NC_015762.1| Bombus terrestris linkage group LG B01, Bter_1.0 chromosome, whole genome shotgun sequence ...
Code:
bowtie2-inspect -s Flags 1 Reverse flags 5 Colorspace 0 2.0-compatible 1 SA-Sample 1 in 16 FTab-Chars 10 Sequence-1 gi|339751252|ref|NC_015762.1| Bombus terrestris linkage group LG B01, Bter_1.0 chromosome, whole genome shotgun sequence 17153651 ...
Code:
#!gff-spec-version 1.20 #!processor NCBI annotwriter ##sequence-region NC_015762.1 1 17153651 ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=30195 NC_015762.1 RefSeq region 1 17153651 . + . ID=id0;Dbxref=taxon:30195;gbkey=Src;genome=chromosome;linkage-group=LG B01;mol_type=genomic DNA;note=haploid drones;sex=male NC_015762.1 RefSeq gene 2279 19877 . - . ID=gene0;Name=LOC100649911;Dbxref=GeneID:100649911;gbkey=Gene;gene=LOC100649911 ...
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