这是由于你的gtf和参考基因组里面的染色体编号不匹配;检查是否下载错误的gtf
比如有的注释有问题,gff里面基因在染色体上的位置,比染色体都长等等,导致fasta序列提取错误。
tophat建立索引的时候出现报错;
"/share/work/biosoft/tophat/tophat-2.1.1/bin/tophat2" -G Sspon.v20180123.gtf --transcriptome-index=transcriptome_data/known Sspon.HiC_chr_asm
[2019-04-28 05:49:42] Building transcriptome files with TopHat v2.1.1
-----------------------------------------------
[2019-04-28 05:49:42] Checking for Bowtie
Bowtie version: 2.2.7.0
[2019-04-28 05:49:44] Checking for Bowtie index files (genome)..
Found both Bowtie1 and Bowtie2 indexes.
[2019-04-28 05:49:44] Checking for reference FASTA file
[2019-04-28 05:49:44] Building transcriptome data files transcriptome_data/known
[FAILED]
Error: gtf_to_fasta returned an error.