ABCDEFGHIJKLMNOPQRSTUVWXYZ
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Speciedbkeybowtie-indexbowtie2bwa_indexliftoverrsem.2bit.fa.fa.faigtfgff
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arabidopsis thaliana at9yesyesyesyesyesyesyesyes
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201620162016201602/01/201802/01/2018
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from ensembl
ftp://ftp.ensemblgenom
es.org/pub/release-38/
plants/gtf/arabidopsis_
thaliana/		 from
TAIR portal https://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FGenes
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at10yesyesyesyesyesyesyesyes
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20162016201602/01/201802/01/2018
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from Federico (2016)from Federico (2016)from ensembl
ftp://ftp.ensemblgenom
es.org/pub/release-38/
plants/gtf/arabidopsis_
thaliana/		 from
TAIR portal https://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FGenes
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drosophila melanogasterdm2yesno
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2016
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dm3yesyesyesyesyesyesyesyesyesno
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201620162016201611/03/201820162016201611/03/2018
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1 Mar 2018 (mtangaro) - Added dm3ToDm6.over.chain from http://hgdownload.soe.ucsc.edu/goldenPath/dm3/liftOver/rsem version: 1.3.0
command: rsem-prepare-reference --gtf (.gtf) --transcript-to-gene-map (table.txt) --bowtie (.fa) dm6
.fa download date:11/03/2018
.fa download url: from ucsc http://hgdownload.cse.ucsc.edu/goldenPath/ for assembly that does not have
all the genome in fasta format were downloaded the .2bit format and converted in .fa using the ucsc tool fatotwobit
link of the program https://genome.ucsc.edu/goldenpath/help/twoBit.html
gtf download date: 11/03/2018
gtf download link: ucsc tablebrowser
table download date 11/03/2018
table download link : https://genome.ucsc.edu/cgi-bin/hgTables
Select Fields from "genome".refGene--> name
genome.refFlat fields -->geneName
Linked Tables--> refFlat
the table and the .gtf must be downloaded the same day
from ucsc table
browser https://genom
e.ucsc.edu/cgi-bin/hg
Tables
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Homo sapienshg18yesyesyesyesyesyesyesyesyesno
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201620162016201611/03/2018
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rsem version: 1.3.0
command: rsem-prepare-reference --gtf (.gtf) --transcript-to-gene-map (table.txt) --bowtie (.fa) dm6
.fa download date:11/03/2018
.fa download url: from ucsc http://hgdownload.cse.ucsc.edu/goldenPath/ for assembly that does not have
all the genome in fasta format were downloaded the .2bit format and converted in .fa using the ucsc tool fatotwobit
link of the program https://genome.ucsc.edu/goldenpath/help/twoBit.html
gtf download date: 11/03/2018
gtf download link: ucsc tablebrowser
table download date 11/03/2018
table download link : https://genome.ucsc.edu/cgi-bin/hgTables
Select Fields from "genome".refGene--> name
genome.refFlat fields -->geneName
Linked Tables--> refFlat
the table and the .gtf must be downloaded the same day		from Federico (2016)from Federico (2016)from Federico (2016)
from ucsc table
browser https://genom
e.ucsc.edu/cgi-bin/hg
Tables
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hg19yesyesyesyesyesyesyesyesyesno
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201620162016201611/03/2018
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rsem version: 1.3.0
command: rsem-prepare-reference --gtf (.gtf) --transcript-to-gene-map (table.txt) --bowtie (.fa) dm6
.fa download date:11/03/2018
.fa download url: from ucsc http://hgdownload.cse.ucsc.edu/goldenPath/ for assembly that does not have
all the genome in fasta format were downloaded the .2bit format and converted in .fa using the ucsc tool fatotwobit
link of the program https://genome.ucsc.edu/goldenpath/help/twoBit.html
gtf download date: 11/03/2018
gtf download link: ucsc tablebrowser
table download date 11/03/2018
table download link : https://genome.ucsc.edu/cgi-bin/hgTables
Select Fields from "genome".refGene--> name
genome.refFlat fields -->geneName
Linked Tables--> refFlat
the table and the .gtf must be downloaded the same day		from Federico (2016)from Federico (2016)from Federico (2016)
from ucsc table
browser https://genom
e.ucsc.edu/cgi-bin/hg
Tables
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hg38yesyesyesyesyesyesyesyesyesyes
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from Federico (2016)from Federico (2016)from Federico (2016)from Federico (2016)11/03/201820162016from Federico (2016)11/03/201814/01/2018
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rsem version: 1.3.0
command: rsem-prepare-reference --gtf (.gtf) --transcript-to-gene-map (table.txt) --bowtie (.fa) dm6
.fa download date:11/03/2018
.fa download url: from ucsc http://hgdownload.cse.ucsc.edu/goldenPath/ for assembly that does not have
all the genome in fasta format were downloaded the .2bit format and converted in .fa using the ucsc tool fatotwobit
link of the program https://genome.ucsc.edu/goldenpath/help/twoBit.html
gtf download date: 11/03/2018
gtf download link: ucsc tablebrowser
table download date 11/03/2018
table download link : https://genome.ucsc.edu/cgi-bin/hgTables
Select Fields from "genome".refGene--> name
genome.refFlat fields -->geneName
Linked Tables--> refFlat
the table and the .gtf must be downloaded the same day
from ucsc table
browser https://genom
e.ucsc.edu/cgi-bin/hg
Tables		pietro 14.01.2018 from
ensemble portal
ftp://ftp.ensembl.org/pub/release-91/gff3/
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mus musculusmm8yesno
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from Federico (2016)
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mm9yesyesyesyesyesyesyesyesyesno
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201620162016201611/03/2018from Federico (2016)from Federico (2016)from Federico (2016)11/03/2018
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rsem version: 1.3.0
command: rsem-prepare-reference --gtf (.gtf) --transcript-to-gene-map (table.txt) --bowtie (.fa) dm6
.fa download date:11/03/2018
.fa download url: from ucsc http://hgdownload.cse.ucsc.edu/goldenPath/ for assembly that does not have
all the genome in fasta format were downloaded the .2bit format and converted in .fa using the ucsc tool fatotwobit
link of the program https://genome.ucsc.edu/goldenpath/help/twoBit.html
gtf download date: 11/03/2018
gtf download link: ucsc tablebrowser
table download date 11/03/2018
table download link : https://genome.ucsc.edu/cgi-bin/hgTables
Select Fields from "genome".refGene--> name
genome.refFlat fields -->geneName
Linked Tables--> refFlat
the table and the .gtf must be downloaded the same day
from ucsc table
browser https://genom
e.ucsc.edu/cgi-bin/hg
Tables
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mm10yesyesyesyesyesyesyesyesyesyes
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201620162016201611/03/20182016201611/03/201811/03/201814/01/2018
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mm10ToHg19.over.chain mm10ToMm9.over.chainrsem version: 1.3.0
command: rsem-prepare-reference --gtf (.gtf) --transcript-to-gene-map (table.txt) --bowtie (.fa) dm6
.fa download date:11/03/2018
.fa download url: from ucsc http://hgdownload.cse.ucsc.edu/goldenPath/ for assembly that does not have
all the genome in fasta format were downloaded the .2bit format and converted in .fa using the ucsc tool fatotwobit
link of the program https://genome.ucsc.edu/goldenpath/help/twoBit.html
gtf download date: 11/03/2018
gtf download link: ucsc tablebrowser
table download date 11/03/2018
table download link : https://genome.ucsc.edu/cgi-bin/hgTables
Select Fields from "genome".refGene--> name
genome.refFlat fields -->geneName
Linked Tables--> refFlat
the table and the .gtf must be downloaded the same day
from ucsc table
browser https://genom
e.ucsc.edu/cgi-bin/hg
Tables		 from
ensemble portal
ftp://ftp.ensembl.org/pub/release-91/gff3/
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Saccharomyces cerevisiaesacCer1yes
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2016
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sacCer1ToSacCer2.over.chain sacCer1ToSacCer3.over.chain
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sacCer2yes
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2016
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sacCer2ToSacCer3.over.chain
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sacCer3yesyesyesyesyesyesyesyesyesyes
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201620162016201611/03/201820162016201611/03/201814/01/2018
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sacCer3ToSacCer2.over.chain

rsem version: 1.3.0
command: rsem-prepare-reference --gtf (.gtf) --transcript-to-gene-map (table.txt) --bowtie (.fa) dm6
.fa download date:11/03/2018
.fa download url: from ucsc http://hgdownload.cse.ucsc.edu/goldenPath/ for assembly that does not have
all the genome in fasta format were downloaded the .2bit format and converted in .fa using the ucsc tool fatotwobit
link of the program https://genome.ucsc.edu/goldenpath/help/twoBit.html
gtf download date: 11/03/2018
gtf download link: ucsc tablebrowser
table download date 11/03/2018
table download link : https://genome.ucsc.edu/cgi-bin/
Select Fields from sacCer3.sgdGene --> name
Linked Tables --> sdgtoname
sacCer3.sgdToName fields --> value
the table and the .gtf must be downloaded the same day
from ucsc table
browser https://genom
e.ucsc.edu/cgi-bin/hg
Tables		pietro 14.01.2018 from
ensemble portal
ftp://ftp.ensembl.org/pub/release-91/gff3/
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drosophila melanogasterdm6yesyesyesyesyesyesyesyesyes
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02/02/201822/01/201819/01/201801/03/201811/03/201802/03/201801/03/201811/03/201814/01/2018
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Bowtie (1.2.0) from conda.Bowtie2 (2.3.0) from conda1 Mar 2018 (mtangaro) - Added dm6ToDm3.over.chain from http://hgdownload.soe.ucsc.edu/goldenPath/dm6/liftOver/
Still to add to CVMFS server 90.147.102.186

rsem version: 1.3.0
command: rsem-prepare-reference --gtf (.gtf) --transcript-to-gene-map (table.txt) --bowtie (.fa) dm6
.fa download date:11/03/2018
.fa download url: from ucsc http://hgdownload.cse.ucsc.edu/goldenPath/ for assembly that does not have
all the genome in fasta format were downloaded the .2bit format and converted in .fa using the ucsc tool fatotwobit
link of the program https://genome.ucsc.edu/goldenpath/help/twoBit.html
gtf download date: 11/03/2018
gtf download link: ucsc tablebrowser
table download date 11/03/2018
table download link : https://genome.ucsc.edu/cgi-bin/hgTables
Select Fields from "genome".refGene--> name
genome.refFlat fields -->geneName
Linked Tables--> refFlat
the table and the .gtf must be downloaded the same day
http://hgdownload.cse.ucsc.edu/goldenPath/dm6/bigZips/dm6.2bithttp://hgdownload.cse.ucsc.edu/goldenPath/dm6/bigZips/dm6.fa.gzfrom ucsc table
browser https://genom
e.ucsc.edu/cgi-bin/hg
Tables		pietro 14.01.2018 from
ensemble portal
ftp://ftp.ensembl.org/pub/release-91/gff3/
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indices created with fasta file downloaded from tablebrowser ucsc from terminal with the command:

(__bowtie@1.2.0) (.venv) [galaxy@galaxy-server bin]$ ./bowtie-build /export/dm6fasta/dm6.fa dm6
.gtf files were cleaned to get rsem_index and better annotation
cleaning method:
1) executed the script chr_list.py to have the list of chromosome of the .gtf
→ command python chr_list.py file.gtf
2) deleted the extra-chromosome lines using sed (from terminal: sed -i ‘/’extra-chromosome’/d’ file.gtf)
3) executed the rewrite_gtf.py redirecting the output to a file.gtf
→ command python rewrite_gtf.py file.gtf>new_file.gtf
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