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Description
Hi, your work is so excellent! But I met several problems.
I used Hisat2 (GRCh37 index genome_tran_snp)to mapping the fastq file.
In the hisat2 index create script I found it used Esemble fasta and gtf.
So I download "Homo_sapiens.GRCh37.75.dna.primary_assembly.fa" and "Homo_sapiens.GRCh37.75.gtf" from ensemble ftp.
Then used "grep -P "\tCDS\t" Homo_sapiens.GRCh37.75.gtf | gtf2bed > Homo_sapiens.GRCh37.75.CDS.bed" to create CDS.bed file.
regtools (0.5.0 version)
But when I run my data, it stop in regtools junctions annotate step as below:
I'm sure the fasta and gtf must be same version(37 or 38). But how is the relations between mapping index and your software needed (UCSC, emsemble or NCBI). For my data, I used hisat2 index fasta and gtf from ensemble to mapping, though I used same reference in your software as input, but it is error. Is it suitable to use UCSC in your software? Could you help me to analyse these problems, Thank you very much!