diff --git a/docs/references.md b/docs/references.md
new file mode 100644
index 0000000..e904632
--- /dev/null
+++ b/docs/references.md
@@ -0,0 +1,413 @@
+## circRNA DAQ Pipeline
+
+
+
+The reference sequences comprises of the host genome and the viral genomes.
+
+### Fasta
+
+*hg38* genome build is chosen to represent human (host). Human ribosomal sequences (*45S, 5S*) are downloaded from NCBI. *hg38* was masked for rRNA sequence and *45S* and *5S* sequences from NCBI are appended as separate chromosomes. The following viral sequences were appended to the rRNA masked *hg38* reference:
+
+| RefSeq Sequence | RefSeq assembly accession | Notes |
+| ---------------- | ------------------------- | ----------------------------------------------------- |
+| NC_007605.1 | GCF_002402265.1 | Human gammaherpesvirus 4 (Epstein-Barr virus) |
+| NC_000898.1 | GCF_000846365.1 | Human betaherpesvirus 6B |
+| NC_001664.4 | GCF_000845685.2 | Human betaherpesvirus 6A |
+| NC_001716.2 | GCF_000848125.1 | Human betaherpesvirus 7 |
+| NC_006273.2 | GCF_000845245.1 | Human betaherpesvirus 5 |
+| NC_009333.1 | GCF_000838265.1 | Human gammaherpesvirus 8 |
+| NC_045512.2 | GCF_009858895.2 | Severe acute respiratory syndrome-related coronavirus |
+| MN485971.1 | xx | HIV from Belgium ... GTF is hand curated |
+
+Location: The entire resource bundle is available at `/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC` on biowulf. This location also have additional bash scritpts required for aggregating annotations and building indices required by different aligners.
+
+**Update** **(02/10/21)**
+
+The following viral sequence has also been appended to the reference:
+
+| RefSeq Sequence | RefSeq assembly accession | Notes |
+| ---------------- | ------------------------- | ------------------------------------------------------------ |
+| NC_001806.2 | GCF_000859985.2 | [Human alphaherpesvirus 1 (Herpes simplex virus type 1)](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=10298&lvl=3&lin=f&keep=1&srchmode=1&unlock) (strain 17) |
+
+Location: The updated resource bundle is at `/data/Ziegelbauer_lab/resources/hg38_rRNA_masked_plus_rRNA_plus_viruses_plus_ERCC.v2` on biowulf
+
+### Annotations
+
+Gencode release 36 is used to annotate the human transcripts. Customized RefSeq annotations are used for annotating the viral sequences.
+
+#### Viruses
+
+To properly annotate viral sequences the following process was followed:
+
+**Downloading annotations from NCBI:**
+
+For example, to download gtf annotations for KSHV genome search "KSHV" at [NCBI](https://www.ncbi.nlm.nih.gov/assembly/)
+
+
+
+On the results page (assembly page), click on "FTP directory for RefSeq assembly"
+
+
+
+The FTP page has the relevant sequence and annotations files:
+
+
+
+Download the file ending with *.gtf.gz*:
+
+```bash
+> curl -L "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/838/265/GCF_000838265.1_ViralProj14158/GCF_000838265.1_ViralProj14158_genomic.gtf.gz" > GCF_000838265.1_ViralProj14158_genomic.gtf.gz
+
+> gzip -d GCF_000838265.1_ViralProj14158_genomic.gtf.gz
+```
+
+**What needs to be fixed?**
+
+The GTF file downloaded from NBCI (RefSeq annotations) needs fixing in order to work seemlessly with STAR and CCBR_Pipeliner:
+
+1. GTF is missing lines for "transcript" in column 3. Transcript coordinates can be different from "gene" coordinates. I am going to pick all non-"gene" lines for a particular gene, filter them for a particular "transcript", ~~find the leftmost and rightmost coordinate and use them as coordinates for the new "transcript" line in the new GTF file~~. Using leftmost and rightmost script eliminates the UTR regions and hence if a gene has only one transcript (most common scenario), the transcript coordinates mimic the gene coordinates.
+ eg. for **HHV8GK18_gp01** gene these are the lines in the original file
+
+ ```bash
+ NC_009333.1 RefSeq gene 4 1083 . + . gene_id "HHV8GK18_gp01"; db_xref "GeneID:4961511"; gbkey "Gene"; gene "K1"; gene_biotype "protein_coding"; locus_tag "HHV8GK18_gp01";
+ NC_009333.1 RefSeq exon 29 1083 . + . gene_id "HHV8GK18_gp01"; transcript_id "HHV8GK18_gp01"; gbkey "mRNA"; gene "K1"; locus_tag "HHV8GK18_gp01"; exon_number "1";
+ NC_009333.1 RefSeq CDS 105 941 . + 0 gene_id "HHV8GK18_gp01"; transcript_id "HHV8GK18_gp01"; gbkey "CDS"; gene "K1"; locus_tag "HHV8GK18_gp01"; note "contains an Ig domain"; product "K1"; protein_id "YP_001129350.1"; exon_number "1";
+ NC_009333.1 RefSeq start_codon 105 107 . + 0 gene_id "HHV8GK18_gp01"; transcript_id "HHV8GK18_gp01"; gbkey "CDS"; gene "K1"; locus_tag "HHV8GK18_gp01"; note "contains an Ig domain"; product "K1"; protein_id "YP_001129350.1"; exon_number "1";
+ NC_009333.1 RefSeq stop_codon 942 944 . + 0 gene_id "HHV8GK18_gp01"; transcript_id "HHV8GK18_gp01"; gbkey "CDS"; gene "K1"; locus_tag "HHV8GK18_gp01"; note "contains an Ig domain"; product "K1"; protein_id "YP_001129350.1"; exon_number "1";
+ ```
+
+2. Some transcripts have ids as "unknown_transcript_1". New name will be of the format "**gene_id**+_transcript_1". All child features for the transcript in question need the **transcript_id** to be changed to the new name.
+
+ ```bash
+ NC_009333.1 RefSeq gene 3179 17026 . + . gene_id "HHV8GK18_gp03"; db_xref "GeneID:4961521"; gbkey "Gene"; gene "ORF6"; gene_biotype "protein_coding"; locus_tag "HHV8GK18_gp03";
+ NC_009333.1 RefSeq CDS 3179 6574 . + 0 gene_id "HHV8GK18_gp03"; transcript_id "unknown_transcript_1"; gbkey "CDS"; gene "ORF6"; locus_tag "HHV8GK18_gp03"; note "herpesvirus core gene UL29 family"; product "ORF6"; protein_id "YP_001129352.1";
+ NC_009333.1 RefSeq start_codon 3179 3181 . + 0 gene_id "HHV8GK18_gp03"; transcript_id "unknown_transcript_1"; gbkey "CDS"; gene "ORF6"; locus_tag "HHV8GK18_gp03"; note "herpesvirus core gene UL29 family"; product "ORF6"; protein_id "YP_001129352.1";
+ NC_009333.1 RefSeq stop_codon 6575 6577 . + 0 gene_id "HHV8GK18_gp03"; transcript_id "unknown_transcript_1"; gbkey "CDS"; gene "ORF6"; locus_tag "HHV8GK18_gp03"; note "herpesvirus core gene UL29 family"; product "ORF6"; protein_id "YP_001129352.1";
+ ```
+
+3. Some **gene_id** 's are empty. I am planning on reporting these in a separate file ending with *.extralines*. These need to be edited manually and appended to the output GTF file. I will be using "chromosome_name:start_coordinate-end_coordinate" as the format for generating a unique **gene_id** for replacement GTF entries. Eg.
+
+ ```bash
+ NC_009333.1 RefSeq exon 118075 118097 . - . gene_id ""; transcript_id "unknown_transcript_1"; gbkey "misc_RNA"; product "miR-K10"; exon_number "1";
+ NC_009333.1 RefSeq exon 127997 129368 . + . gene_id ""; transcript_id "unknown_transcript_1"; gbkey "mRNA"; note "K14, ORF74; polyA_site not reported"; exon_number "1";
+ NC_009333.1 RefSeq exon 129517 130671 . + . gene_id ""; transcript_id "unknown_transcript_1"; gbkey "mRNA"; note "K14, ORF74; polyA_site not reported"; exon_number "2";
+ ```
+
+ will be changed to something like this:
+
+ ```bash
+ NC_009333.1 RefSeq gene 118075 118097 . - . gene_id "NC_009333.1:118075-118097"; gene_name "NC_009333.1:118075-118097"; gene_biotype "miRNA"; gbkey "misc_RNA"; product "miR-K10";
+ NC_009333.1 RefSeq transcript 118075 118097 . - . gene_id "NC_009333.1:118075-118097"; gene_name "NC_009333.1:118075-118097"; gene_biotype "miRNA"; transcript_id "NC_009333.1:118075-118097_
+ transcript_1"; transcript_name "NC_009333.1:118075-118097_transcript_1"; transcript_type "miRNA"; gbkey "misc_RNA"; product "miR-K10";
+ NC_009333.1 RefSeq exon 118075 118097 . - . gene_id "NC_009333.1:118075-118097"; transcript_id "NC_009333.1:118075-118097_transcript_1"; gbkey "misc_RNA"; product "miR-K10"; exon_number "1";
+ NC_009333.1 RefSeq gene 127997 130671 . + . gene_id "NC_009333.1:127997_130671"; gene_name "NC_009333.1:127997_130671"; gene_biotype "mRNA"; gbkey "mRNA"; note "K14, ORF74; polyA_site not reporte
+ d";
+ NC_009333.1 RefSeq transcript 127997 130671 . + . gene_id "NC_009333.1:127997_130671"; gene_name "NC_009333.1:127997_130671"; gene_biotype "mRNA"; transcript_id "NC_009333.1:127997_130671_transcr
+ ipt_1"; transcript_name "NC_009333.1:127997_130671_transcript_1"; transcript_type "NC_009333.1:127997_130671_transcript_1";gbkey "mRNA"; note "K14, ORF74; polyA_site not reported";
+ NC_009333.1 RefSeq exon 127997 129368 . + . gene_id "NC_009333.1:127997_130671"; transcript_id "NC_009333.1:127997_130671_transcript_1"; gbkey "mRNA"; note "K14, ORF74; polyA_site not reported";
+ exon_number "1";
+ NC_009333.1 RefSeq exon 129517 130671 . + . gene_id "NC_009333.1:127997_130671"; transcript_id "NC_009333.1:127997_130671_transcript_1"; gbkey "mRNA"; note "K14, ORF74; polyA_site not reported";
+ exon_number "2";
+ ```
+
+4. Only few genes have **exon** features. Most of them have **CDS** only. The **exon** line is added to have coordinates same as the **CDS**, if it is missing.
+
+ eg. This
+
+ ```bash
+ NC_009333.1 RefSeq gene 15756 17026 . + . gene_id "HHV8GK18_gp08"; gene_name "ORF11"; gene_biotype "protein_coding"; db_xref "GeneID:4961439"; gbkey "Gene"; locus_tag "HHV8GK18_gp08";
+ NC_009333.1 RefSeq transcript 15756 16979 . + . gene_id "HHV8GK18_gp08"; gene_name "ORF11"; gene_biotype "protein_coding"; transcript_id "HHV8GK18_gp08_transcript_1"; transcript_name "HHV8GK18_gp08_transcript_1"; transcript_type "protein_coding";
+ NC_009333.1 RefSeq CDS 15756 16976 . + 0 gene_id "HHV8GK18_gp08"; transcript_id "HHV8GK18_gp08_transcript_1"; gbkey "CDS"; gene "ORF11"; locus_tag "HHV8GK18_gp08"; note "derived from herpesvirus dUTPase; related to HHV-5 UL82, UL83 and UL84"; product "ORF11"; protein_id "YP_001129357.1";
+ NC_009333.1 RefSeq start_codon 15756 15758 . + 0 gene_id "HHV8GK18_gp08"; transcript_id "HHV8GK18_gp08_transcript_1"; gbkey "CDS"; gene "ORF11"; locus_tag "HHV8GK18_gp08"; note "derived from herpesvirus dUTPase; related to HHV-5 UL82, UL83 and UL84"; product "ORF11"; protein_id "YP_001129357.1";
+ NC_009333.1 RefSeq stop_codon 16977 16979 . + 0 gene_id "HHV8GK18_gp08"; transcript_id "HHV8GK18_gp08_transcript_1"; gbkey "CDS"; gene "ORF11"; locus_tag "HHV8GK18_gp08"; note "derived from herpesvirus dUTPase; related to HHV-5 UL82, UL83 and UL84"; product "ORF11"; protein_id "YP_001129357.1";
+ ```
+
+ becomes
+
+ ```bash
+ NC_009333.1 RefSeq gene 15756 17026 . + . gene_id "HHV8GK18_gp08"; gene_name "ORF11"; gene_biotype "protein_coding"; db_xref "GeneID:4961439"; gbkey "Gene"; locus_tag "HHV8GK18_gp08";
+ NC_009333.1 RefSeq transcript 15756 16979 . + . gene_id "HHV8GK18_gp08"; gene_name "ORF11"; gene_biotype "protein_coding"; transcript_id "HHV8GK18_gp08_transcript_1"; transcript_name "HHV8GK18_gp08_transcript_1"; transcript_type "protein_coding";
+ NC_009333.1 RefSeq exon 15756 16976 . + . gene_id "HHV8GK18_gp08"; transcript_id "HHV8GK18_gp08_transcript_1"; gbkey "CDS"; gene "ORF11"; locus_tag "HHV8GK18_gp08"; note "derived from herpesvirus dUTPase; related to HHV-5 UL82, UL83 and UL84"; product "ORF11"; protein_id "YP_001129357.1";
+ NC_009333.1 RefSeq CDS 15756 16976 . + 0 gene_id "HHV8GK18_gp08"; transcript_id "HHV8GK18_gp08_transcript_1"; gbkey "CDS"; gene "ORF11"; locus_tag "HHV8GK18_gp08"; note "derived from herpesvirus dUTPase; related to HHV-5 UL82, UL83 and UL84"; product "ORF11"; protein_id "YP_001129357.1";
+ NC_009333.1 RefSeq start_codon 15756 15758 . + 0 gene_id "HHV8GK18_gp08"; transcript_id "HHV8GK18_gp08_transcript_1"; gbkey "CDS"; gene "ORF11"; locus_tag "HHV8GK18_gp08"; note "derived from herpesvirus dUTPase; related to HHV-5 UL82, UL83 and UL84"; product "ORF11"; protein_id "YP_001129357.1";
+ NC_009333.1 RefSeq stop_codon 16977 16979 . + 0 gene_id "HHV8GK18_gp08"; transcript_id "HHV8GK18_gp08_transcript_1"; gbkey "CDS"; gene "ORF11"; locus_tag "HHV8GK18_gp08"; note "derived from herpesvirus dUTPase; related to HHV-5 UL82, UL83 and UL84"; product "ORF11"; protein_id "YP_001129357.1";
+ ```
+
+**Python script to automate:**
+
+Simple python script take in RefSeq's GTF and spits out new GTF. This script (*fix_refseq_gtf.py*) is provided in the scripts folder of the repo.:
+
+```python
+# Author: Vishal N. Koparde
+# CCBR NCI
+# Date: Aug, 2020
+
+
+import sys,copy,argparse
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument('-i',dest='ingtf', required=True, type=str, help="Input RefSeq GTF ..downloaded from NCBI ftp server")
+parser.add_argument('-o',dest='outgtf', required=True, type=str, help="Modified Output RefSeq GTF")
+args = parser.parse_args()
+
+def get_gene_id(column9):
+ x=column9.strip().split()
+ for i,value in enumerate(x):
+ if value=="gene_id":
+ gene_id_index=i+1
+ break
+ gene_id=x[gene_id_index]
+ return gene_id
+
+def get_gene_biotype(column9):
+ x=column9.strip().split()
+ found=0
+ for i,value in enumerate(x):
+ if value=="gene_type" or value=="gene_biotype":
+ gene_biotype_index=i+1
+ found=1
+ break
+ if found==0:
+ return '"unknown";'
+ gene_biotype=x[gene_biotype_index]
+ return gene_biotype
+
+def get_gene_name(column9):
+ x=column9.strip().split()
+ found=0
+ for i,value in enumerate(x):
+ if value=="gene" or value=="gene_name":
+ gene_index=i+1
+ found=1
+ break
+ if found==0:
+ return ""
+ gene_name=x[gene_index]
+ return gene_name
+
+def get_transcript_id(column9):
+ x=column9.strip().split()
+ found=0
+ for i,value in enumerate(x):
+ if value=="transcript_id":
+ transcript_id_index=i+1
+ found=1
+ break
+ if found==0:
+ return '"transcript_id_unknown";'
+ transcript_id=x[transcript_id_index]
+ return transcript_id
+
+def fix_transcript_id(column9,g):
+ x=column9.strip().split()
+ found=0
+ for i,value in enumerate(x):
+ if value=="transcript_id":
+ transcript_id_index=i+1
+ found=1
+ break
+ x[transcript_id_index]=g
+ if found==0:
+ x.append("transcript_id")
+ x.append(g)
+ x=" ".join(x)
+ return x
+
+def create_new_transript_id(g,i):
+ n=g.split('"')
+ n[-2]+="_transcript_"+str(i)
+ n='"'.join(n)
+ return n
+
+def are_exons_present(transcript_lines):
+ for l in transcript_lines:
+ l_split=l.strip().split("\t")
+ if l_split[2]=="exon":
+ return True
+ else:
+ return False
+
+#create genelist
+genelist=[]
+gene_coords=dict()
+all_gtflines=list(filter(lambda x:not x.startswith("#"),open(args.ingtf).readlines()))
+blank_gene_id_lines=[]
+for f in all_gtflines:
+ its_a_gene=0
+ if f.strip().split("\t")[2]=="gene":
+ its_a_gene=1
+ gene_id=get_gene_id(f.strip().split("\t")[8])
+ if gene_id=='"";':
+ blank_gene_id_lines.append(f)
+ continue
+ genelist.append(gene_id)
+ if its_a_gene==1 and not gene_id in gene_coords:
+ gene_coords[gene_id]=(int(f.strip().split("\t")[3]),int(f.strip().split("\t")[4]))
+genelist=list(set(genelist))
+# print(genelist)
+# print(len(blank_gene_id_lines))
+
+#get genes2transcripts ... this is only for verifying that every gene has only 1 transript... this is the assumption
+gene_id_2_transcript_ids=dict()
+for g in genelist:
+ if not g in gene_id_2_transcript_ids:
+ gene_id_2_transcript_ids[g]=list()
+ lines_with_gene_id=list(filter(lambda x: g in x,all_gtflines))
+ non_gene_lines=list(filter(lambda x:x.split("\t")[2]!="gene",lines_with_gene_id))
+ for l in non_gene_lines:
+ t_id=get_transcript_id(l.strip().split("\t")[8])
+ if t_id!='"transcript_id_unknown";':
+ gene_id_2_transcript_ids[g].append(t_id)
+ gene_id_2_transcript_ids[g]=list(set(gene_id_2_transcript_ids[g]))
+
+geneid2transcriptidfile=open(args.ingtf+".geneid2transcriptid",'w')
+for k,v in gene_id_2_transcript_ids.items():
+ geneid2transcriptidfile.write("%s\t%s\n"%(k,v))
+geneid2transcriptidfile.close()
+
+#get genenames
+gene_id_2_gene_name=dict()
+for g in genelist:
+ if not g in gene_id_2_gene_name:
+ gene_id_2_gene_name[g]=list()
+ lines_with_gene_id=list(filter(lambda x: g in x,all_gtflines))
+ gene_line=list(filter(lambda x:x.split("\t")[2]=="gene",lines_with_gene_id))
+ # if len(gene_line)==0:
+ # for l in lines_with_gene_id:
+ # print(l,)
+ gene_line=gene_line[0]
+ gene_name=get_gene_name(gene_line.split("\t")[8])
+ if gene_name=="":
+ gene_name=g
+ gene_id_2_gene_name[g]=gene_name
+# for k,v in gene_id_2_gene_name.items():
+# print(k,v)
+
+#get transcript coordinates
+gene_id_2_transcript_coordinates=dict()
+for g in genelist:
+ # print("gene=",g)
+ if not g in gene_id_2_transcript_coordinates:
+ gene_id_2_transcript_coordinates[g]=list()
+ if len(gene_id_2_transcript_ids[g])==1:
+ gene_id_2_transcript_coordinates[g].append(gene_coords[g])
+ else:
+ lines_with_gene_id=list(filter(lambda x: g in x,all_gtflines))
+ non_gene_lines=list(filter(lambda x:x.split("\t")[2]!="gene",lines_with_gene_id))
+ for t in gene_id_2_transcript_ids[g]:
+ # print("transcript=",t)
+ transcript_lines=list(filter(lambda x:t in x,non_gene_lines))
+ coords=[]
+ for l in transcript_lines:
+ # print(l.strip())
+ l_split=l.split("\t")
+ coords.append(int(l_split[3]))
+ coords.append(int(l_split[4]))
+ # print()
+ gene_id_2_transcript_coordinates[g].append((min(coords),max(coords)))
+ # print(gene_id_2_transcript_coordinates[g])
+# for k,v in gene_id_2_transcript_coordinates.items():
+ # print(k,v)
+# exit()
+
+#get gene biotype\
+gene_id_2_gene_biotype=dict()
+for g in genelist:
+ lines_with_gene_id=list(filter(lambda x: g in x,all_gtflines))
+ gene_line=list(filter(lambda x:x.split("\t")[2]=="gene",lines_with_gene_id))
+ gene_line=gene_line[0]
+ gene_biotype=get_gene_biotype(gene_line.split("\t")[8])
+ gene_id_2_gene_biotype[g]=gene_biotype
+# for k,v in gene_id_2_gene_biotype.items():
+# print(k,v)
+
+out=open(args.outgtf,'w')
+for g in genelist:
+ lines_with_gene_id=list(filter(lambda x: g in x,all_gtflines))
+ gene_line=list(filter(lambda x:x.split("\t")[2]=="gene",lines_with_gene_id))
+ gene_line=gene_line[0]
+ gene_line=gene_line.split("\t")
+ others=gene_line.pop(-1)
+ gene_line_copy=copy.copy(gene_line)
+ # other key value pairs to add in the gene_line(col9)
+ others_to_add=[]
+ # print("others=",others)
+ for o in others.strip().split("; "):
+ # print("o=",o)
+ o2=o.split(" ")
+ # print("o2=",o2)
+ key=o2[0]
+ value=o2[1:]
+ value=" ".join(value)
+ # print("key=",key)
+ # print("value=",value)
+ if key in ["gene_id","gene","gene_name","gene_type","gene_biotype"]:
+ continue
+ else:
+ others_to_add.append(key)
+ if not ";" in value:
+ others_to_add.append(value+";")
+ else:
+ others_to_add.append(value)
+
+ col9=[]
+ col9.append("gene_id")
+ col9.append(g)
+ col9.append("gene_name")
+ col9.append(gene_id_2_gene_name[g])
+ col9.append("gene_biotype")
+ col9.append(gene_id_2_gene_biotype[g])
+ col9plus=copy.copy(col9)
+ col9plus.extend(others_to_add)
+ gene_col9=" ".join(col9plus)
+ gene_line.append(gene_col9)
+ gene_line="\t".join(gene_line)
+ out.write("%s\n"%(gene_line))
+
+ non_gene_lines=list(filter(lambda x:x.split("\t")[2]!="gene",lines_with_gene_id))
+ for i,t in enumerate(gene_id_2_transcript_ids[g]):
+ transcript_line=copy.copy(gene_line_copy)
+ transcript_line[2]="transcript"
+ transcript_line[3]=str(gene_id_2_transcript_coordinates[g][i][0])
+ transcript_line[4]=str(gene_id_2_transcript_coordinates[g][i][1])
+ new_trascript_id=create_new_transript_id(g,i+1)
+ transcript_col9=copy.copy(col9)
+ transcript_col9.append("transcript_id")
+ transcript_col9.append(new_trascript_id)
+ transcript_col9.append("transcript_name")
+ transcript_col9.append(new_trascript_id)
+ transcript_col9.append("transcript_type")
+ transcript_col9.append(gene_id_2_gene_biotype[g])
+ transcript_col9=" ".join(transcript_col9)
+ transcript_line.append(transcript_col9)
+ transcript_line="\t".join(transcript_line)
+ out.write("%s\n"%(transcript_line))
+
+ transcript_lines=list(filter(lambda x:t in x,non_gene_lines))
+ have_exons=are_exons_present(transcript_lines)
+ for l in transcript_lines:
+ # print(l)
+ l=l.strip().split("\t")
+ tofix=l.pop(-1)
+ l.append(fix_transcript_id(tofix,new_trascript_id))
+ if l[2]=="CDS" and have_exons==False:
+ l2=copy.copy(l)
+ l2[7]="."
+ l2[2]="exon"
+ l2="\t".join(l2)
+ out.write("%s\n"%(l2))
+ l="\t".join(l)
+ out.write("%s\n"%(l))
+ # print(l)
+out.close()
+
+out=open(args.ingtf+".extralines",'w')
+for b in blank_gene_id_lines:
+ out.write(b)
+out.close()
+```
+
+Final versions of the GTF as located here:
+
+`/data/Ziegelbauer_lab/circRNADetection/viral_db/GTF/final_versions`
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index 9fbbc58..cc2b7e9 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -32,4 +32,5 @@ nav:
- Home: index.md
- Flowchart: flowchart.md
- Tutorial: tutorial.md
+ - References: references.md
- Versions: versions.md