Mercurial > repos > charles-bernard > alfa
changeset 15:136bcda2a3de draft
Uploaded
| author | charles-bernard |
|---|---|
| date | Tue, 11 Oct 2016 09:13:59 -0400 |
| parents | f1b2c73cc9c1 |
| children | cbb0a78e61e8 |
| files | test-data/alfa_toy-Biofeatures Distribution.pdf test-data/alfa_toy.bam test-data/alfa_toy.bedgraph test-data/alfa_toy.categories_counts test-data/alfa_toy.gtf test-data/alfa_toy.stranded.index test-data/alfa_toy.unstranded.index tool-data/alfa_genomes_indexes.loc.sample |
| diffstat | 8 files changed, 5 insertions(+), 32 deletions(-) [+] |
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--- a/test-data/alfa_toy.bedgraph Tue Oct 11 09:13:18 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -Chr1 149 199 2 -Chr1 299 349 1 -Chr1 499 549 6 -Chr1 1099 1149 1
--- a/test-data/alfa_toy.categories_counts Tue Oct 11 09:13:18 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -#Category,biotype Counts_in_bam Size_in_genome -CDS,protein_coding 300.0 624.0 -five_prime_utr,protein_coding 75.0 250.5 -three_prime_utr,protein_coding 25.0 126.5 -intergenic,intergenic 100.0 249.0
--- a/test-data/alfa_toy.gtf Tue Oct 11 09:13:18 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -Chr1 ensembl_havana gene 250 1250 . + . gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding"; -Chr1 ensembl_havana transcript 250 1250 . + . gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding"; -Chr1 ensembl_havana exon 375 1000 . + . gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding"; -Chr1 ensembl_havana CDS 375 1000 . + 0 gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding"; -Chr1 ensembl_havana five_prime_utr 250 375 . - . gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding"; -Chr1 ensembl_havana three_prime_utr 1000 1250 . - . gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
--- a/test-data/alfa_toy.stranded.index Tue Oct 11 09:13:18 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -#Chr1 1250 -Chr1 249 374 + protein_coding:gene,transcript -Chr1 249 374 - protein_coding:five_prime_utr -Chr1 374 375 + protein_coding:exon,CDS -Chr1 374 375 - protein_coding:five_prime_utr,three_prime_utr -Chr1 375 999 + protein_coding:exon,CDS -Chr1 375 999 - antisense -Chr1 999 1000 + protein_coding:exon,CDS -Chr1 999 1000 - protein_coding:three_prime_utr -Chr1 1000 1250 + protein_coding:gene,transcript -Chr1 1000 1250 - protein_coding:five_prime_utr,three_prime_utr,exon,CDS
--- a/test-data/alfa_toy.unstranded.index Tue Oct 11 09:13:18 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -#Chr1 1250 -Chr1 249 374 . protein_coding:five_prime_utr,gene,transcript -Chr1 374 375 . protein_coding:five_prime_utr,three_prime_utr,exon,CDS -Chr1 375 999 . protein_coding:exon,CDS -Chr1 999 1000 . protein_coding:three_prime_utr,exon,CDS -Chr1 1000 1250 . protein_coding:five_prime_utr,exon,CDS,three_prime_utr,gene,transcript
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/alfa_genomes_indexes.loc.sample Tue Oct 11 09:13:59 2016 -0400 @@ -0,0 +1,5 @@ +#<species> <version> <release> <value> <dbkey> <name> <prefix> +Arabidopsis_thaliana TAIR10 30 Arabidopsis_t_TAIR10_30 Arabidopsis_t_TAIR10_30 Arabidopsis thaliana: TAIR10 <path_to_alfa_indexes>/Arabidopsis_thaliana.TAIR10.30 +Drosophila_melanogaster dm6 30 Drosophila_m_dm6_30 Drosophila_m_dm6_30 Drosophila melanogaster: dm6 <path_to_alfa_indexes>/Drosophila_melanogaster.BDGP6.30 +Homo_sapiens v38 82 Homo_s_v38_82 Homo_s_v38_82 Homo sapiens: v38 <path_to_alfa_indexes>/Homo_sapiens.GRCh38.82 +Mus_musculus v38 83 Mus_m_v38_83 Mus_m_v38_83 Mus musculus: v38 <path_to_alfa_indexes>/Mus_musculus.GRCm38.83.chr \ No newline at end of file