# HG changeset patch # User iuc # Date 1430275594 14400 # Node ID c5fe1886445a6f867c1d6f460fdbb4a6e6272409 # Parent 0dda4295f543d8b80e742e6cf89431dd65543d44 Uploaded diff -r 0dda4295f543 -r c5fe1886445a stringtie.xml --- a/stringtie.xml Thu Mar 05 22:41:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,168 +0,0 @@ - - RNA-Seq assembler - - stringtie - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - guide['use_guide'] == "yes" - - - guide['output_ballgown'] - - - guide['output_ballgown'] - - - guide['output_ballgown'] - - - guide['output_ballgown'] - - - guide['output_ballgown'] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - [-G ] [-l ] [-o ] [-p ] - [-v] [-a ] [-m ] [-j ] [-n sens] - [-C ] [-s ] [-c ] [-g ] - {-B | -b } [-e] - -Assemble RNA-Seq alignments into potential transcripts. - - Options: - -G reference annotation to use for guiding the assembly process (GTF/GFF3) - -l name prefix for output transcripts (default: STRG) - -f minimum isoform fraction (default: 0.1) - -m minimum assembled transcript length to report (default 200bp) - -o output path/file name for the assembled transcripts GTF (default: stdout) - -a minimum anchor length for junctions (default: 10) - -j minimum junction coverage (default: 1) - -t disable trimming of predicted transcripts based on coverage - (default: coverage trimming is enabled) - -c minimum reads per bp coverage to consider for transcript assembly (default: 2.5) - -s coverage saturation threshold; further read alignments will be - ignored in a region where a local coverage depth of - is reached (default: 1,000,000); - -v verbose (log bundle processing details) - -g gap between read mappings triggering a new bundle (default: 50) - -C output file with reference transcripts that are covered by reads - -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95) - -p number of threads (CPUs) to use (default: 1) - -B enable output of Ballgown table files which will be created in the - same directory as the output GTF (requires -G, -o recommended) - -b enable output of Ballgown table files but these files will be - created under the directory path given as - -e only estimates the abundance of given reference transcripts (requires -G) - ]]> - - - doi:10.1038/nbt.3122 - - diff -r 0dda4295f543 -r c5fe1886445a test-data/._stringtie_in1.bam Binary file test-data/._stringtie_in1.bam has changed diff -r 0dda4295f543 -r c5fe1886445a test-data/._stringtie_out2.gtf Binary file test-data/._stringtie_out2.gtf has changed diff -r 0dda4295f543 -r c5fe1886445a test-data/ballgown/e2t.ctab --- a/test-data/ballgown/e2t.ctab Thu Mar 05 22:41:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -e_id t_id -1 1 -2 1 -3 1 diff -r 0dda4295f543 -r c5fe1886445a test-data/ballgown/e_data.ctab --- a/test-data/ballgown/e_data.ctab Thu Mar 05 22:41:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -e_id chr strand start end rcount ucount mrcount cov cov_sd mcov mcov_sd -1 test_chromosome + 53 250 154 154 154.00 49.7778 22.0747 49.7778 22.0747 -2 test_chromosome + 351 400 73 73 73.00 54.1600 6.1753 54.1600 6.1753 -3 test_chromosome + 501 550 38 38 38.00 21.6400 12.4350 21.6400 12.4350 diff -r 0dda4295f543 -r c5fe1886445a test-data/ballgown/i2t.ctab --- a/test-data/ballgown/i2t.ctab Thu Mar 05 22:41:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -i_id t_id -1 1 -2 1 diff -r 0dda4295f543 -r c5fe1886445a test-data/ballgown/i_data.ctab --- a/test-data/ballgown/i_data.ctab Thu Mar 05 22:41:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -i_id chr strand start end rcount ucount mrcount -1 test_chromosome + 251 350 49 49 49.00 -2 test_chromosome + 401 500 38 38 38.00 diff -r 0dda4295f543 -r c5fe1886445a test-data/ballgown/t_data.ctab --- a/test-data/ballgown/t_data.ctab Thu Mar 05 22:41:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -t_id chr strand start end t_name num_exons length gene_id gene_name cov FPKM -1 test_chromosome + 53 550 CUFF.1.1 3 298 CUFF.1 . 44.724823 3276543.750000 diff -r 0dda4295f543 -r c5fe1886445a test-data/stringtie_in.gtf --- a/test-data/stringtie_in.gtf Thu Mar 05 22:41:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -test_chromosome Cufflinks transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185"; -test_chromosome Cufflinks exon 53 250 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185"; -test_chromosome Cufflinks exon 351 400 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185"; -test_chromosome Cufflinks exon 501 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185"; diff -r 0dda4295f543 -r c5fe1886445a test-data/stringtie_in1.bam Binary file test-data/stringtie_in1.bam has changed diff -r 0dda4295f543 -r c5fe1886445a test-data/stringtie_out1.gtf --- a/test-data/stringtie_out1.gtf Thu Mar 05 22:41:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.724823";FPKM "3276543.750000"; -test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.011967"; -test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "51.382565"; -test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.090000"; diff -r 0dda4295f543 -r c5fe1886445a test-data/stringtie_out2.gtf --- a/test-data/stringtie_out2.gtf Thu Mar 05 22:41:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.724823";FPKM "3276543.750000"; -test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.011967"; -test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "51.382565"; -test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.090000"; diff -r 0dda4295f543 -r c5fe1886445a test-data/stringtie_out3.gtf --- a/test-data/stringtie_out3.gtf Thu Mar 05 22:41:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; cov "44.724823";FPKM "3276543.750000"; -test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; cov "49.011967"; -test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; cov "51.382565"; -test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; cov "21.090000"; diff -r 0dda4295f543 -r c5fe1886445a test-data/stringtie_out4.gtf --- a/test-data/stringtie_out4.gtf Thu Mar 05 22:41:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; cov "44.724823";FPKM "3276543.750000"; -test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; cov "49.011967"; -test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; cov "51.382565"; -test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; cov "21.090000"; diff -r 0dda4295f543 -r c5fe1886445a test-data/stringtie_out5.gtf --- a/test-data/stringtie_out5.gtf Thu Mar 05 22:41:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; cov "44.724823";FPKM "3276543.750000"; -test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; cov "49.011967"; -test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; cov "51.382565"; -test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; cov "21.090000"; diff -r 0dda4295f543 -r c5fe1886445a test-data/stringtie_out_coverage.gtf --- a/test-data/stringtie_out_coverage.gtf Thu Mar 05 22:41:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -test_chromosome Cufflinks transcript 53 550 1000.00 + . ID=CUFF.1.1;geneID=CUFF.1 -test_chromosome Cufflinks exon 53 250 1000.00 + . Parent=CUFF.1.1 -test_chromosome Cufflinks exon 351 400 1000.00 + . Parent=CUFF.1.1 -test_chromosome Cufflinks exon 501 550 1000.00 + . Parent=CUFF.1.1 diff -r 0dda4295f543 -r c5fe1886445a tool_dependencies.xml --- a/tool_dependencies.xml Thu Mar 05 22:41:06 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - -