diff --git a/README.md b/README.md index 0ff01fdb6..a82f0ba00 100644 --- a/README.md +++ b/README.md @@ -436,6 +436,10 @@ The earth sciences folder contain subfolders for different data formats encounte - plastid - Homo_sapiens.GRCh38.111_chr20_rois.txt: metagene generated from Homo_sapiens.GRCh38.111_chr20.gtf using plastid `metagene generate` command - SRX11780887_p_offsets.txt: p-site offsets genereated from SRX11780887_chr20.bam and Homo_sapiens.GRCh38.111_chr20.gtf using plastid `psite` command + - ribocode + - genome_updated.gtf.gz: GTF with gene names updated via ribocode/gtfupdate, compressed for efficient storage + - annotation.tar.gz: Tarball containing annotation directory output from ribocode/prepare for testing ribocode/metaplots and ribocode/ribocode modules + - test_pre_config.txt: P-site configuration file output from ribocode/metaplots for testing ribocode/ribocode module - salmon.merged.gene_counts_length_scaled.tsv: Example matrix containing both Riboseq and RNA-seq runs, suitable for translational efficiency analysis - samplesheet.csv: Sample sheet corresponding to salmon.merged.gene_counts_length_scaled.tsv - illumina diff --git a/data/genomics/homo_sapiens/riboseq_expression/ribocode/README.md b/data/genomics/homo_sapiens/riboseq_expression/ribocode/README.md new file mode 100644 index 000000000..caed915bf --- /dev/null +++ b/data/genomics/homo_sapiens/riboseq_expression/ribocode/README.md @@ -0,0 +1,21 @@ +# RiboCode module test files + +Intermediate outputs for testing ribocode modules. + +## genome_updated.gtf.gz + +Compressed output from `ribocode/gtfupdate` module. Use with GUNZIP to decompress. + +## annotation.tar.gz + +Tarball of output from `ribocode/prepare` module containing: + +- `transcripts.pickle` - Pickled transcript annotation data +- `transcripts_cds.txt` - CDS information for transcripts +- `transcripts_sequence.fa` - Transcript sequences in FASTA format + +Use with UNTAR module to extract before passing to ribocode modules. + +## test_pre_config.txt + +P-site offset configuration file generated by `ribocode/metaplots` module. diff --git a/data/genomics/homo_sapiens/riboseq_expression/ribocode/annotation.tar.gz b/data/genomics/homo_sapiens/riboseq_expression/ribocode/annotation.tar.gz new file mode 100644 index 000000000..33090bfcf Binary files /dev/null and b/data/genomics/homo_sapiens/riboseq_expression/ribocode/annotation.tar.gz differ diff --git a/data/genomics/homo_sapiens/riboseq_expression/ribocode/genome_updated.gtf.gz b/data/genomics/homo_sapiens/riboseq_expression/ribocode/genome_updated.gtf.gz new file mode 100644 index 000000000..f5211a2bd Binary files /dev/null and b/data/genomics/homo_sapiens/riboseq_expression/ribocode/genome_updated.gtf.gz differ diff --git a/data/genomics/homo_sapiens/riboseq_expression/ribocode/test_pre_config.txt b/data/genomics/homo_sapiens/riboseq_expression/ribocode/test_pre_config.txt new file mode 100644 index 000000000..a72fa2bc9 --- /dev/null +++ b/data/genomics/homo_sapiens/riboseq_expression/ribocode/test_pre_config.txt @@ -0,0 +1,14 @@ + +#SRX11780887.Aligned.toTranscriptome.out.bam +#read_length proportion(per total mapped reads) predicted_psite f0_sum f1_sum f2_sum f0_percent pvalue1 pvalue2 pvalue_combined +# 24 8.99% 11 67 15 12 71.28% 0.07871445393610088 0.05335433821437063 0.016162538604212823 +# 28 15.31% 12 91 20 15 72.22% 0.07861401169693945 0.09699270034475277 0.027516362010860176 +# 29 7.88% 5 24 12 4 60.00% 0.1753983517655281 0.012925525021785452 0.012691976002796142 +# 31 2.24% 4 13 10 2 52.00% 0.21618695127160653 0.0319825310473083 0.031088180227879778 +# 25 12.49% 12 39 20 14 53.42% 0.10425804304619735 0.0065634957174151385 0.004107077153617081 +# 27 16.68% 11 111 18 25 72.08% 0.23199775215455887 0.39876920839246044 0.24221361451859125 +# 30 4.25% 19 22 13 12 46.81% 0.5 0.6184876997235025 0.5844147952291188 +# 26 13.47% 7 72 9 12 77.42% 0.010332180556073796 0.01245294156089251 0.000635986019988928 + +# SampleName AlignmentFile Stranded(yes/reverse) P-siteReadLength P-siteLocations +SRX11780887.Aligned.toTranscriptome.out SRX11780887.Aligned.toTranscriptome.out.bam yes 24,25,26,27,28,29,30,31 11,12,7,11,12,5,19,4