Add files via upload

Author: yuzhuxuyang

README.md

@@ -330,7 +330,7 @@ To identify NMD-targeted transcript isoforms, we first retrieved the sequences o
 2. The transcript contains at least one splice junction
 3. **The 50 nt rule:** The predicted stop codon is $\geq$ 50 nt upstream of the last splice junction (i.e., the transcript harbors a premature termination codon).
 
-We wrote a script, [Translation.sh](./scripts/Translation.sh), that searches for ORFs from transcripts contained in an input file of transcript annotations (GTF format). Our script requires (i) a user-supplied reference genome (FASTA format) and (ii) user-supplied reference transcript annotations (GTF format). Prior to running our script, these files should be placed in the [files](./scripts/Translation_scripts/files/) folder. If you are using the GRCh37/hg19 reference genome build, we recommend using [this reference genome file](https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh37_mapping/GRCh37.primary_assembly.genome.fa.gz) and [this transcript annotation file](https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh37_mapping/gencode.v34lift37.annotation.gtf.gz). Alternatively, if you are using the GRCh38/hg38 reference genome build, we recommend using [this reference genome file](https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/GRCh38.p13.genome.fa.gz) and [this transcript annotation file](https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/gencode.v39.annotation.gtf.gz). 
+We wrote a script, [Translation.sh](./scripts/Translation.sh), that searches for ORFs from transcripts contained in an input file of transcript annotations (GTF format). Our script requires (i) a user-supplied reference genome (FASTA format) and (ii) user-supplied reference transcript annotations (GTF format). Prior to running our script, these files should be placed in the [files](./scripts/scripts/files/) folder. If you are using the GRCh37/hg19 reference genome build, we recommend using [this reference genome file](https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh37_mapping/GRCh37.primary_assembly.genome.fa.gz) and [this transcript annotation file](https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh37_mapping/gencode.v34lift37.annotation.gtf.gz). Alternatively, if you are using the GRCh38/hg38 reference genome build, we recommend using [this reference genome file](https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/GRCh38.p13.genome.fa.gz) and [this transcript annotation file](https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/gencode.v39.annotation.gtf.gz). 
 
 Detailed usage information for our script is shown below: