Trinity - Revision history

Rf at 16:49, 27 January 2017

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Rf at 15:16, 27 January 2017

2017-01-27T15:16:49Z

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@@ Line 81: / Line 81: @@
 Butterfly default reconstruction mode settings
-Note: no CuffFly or PasaFly custom settings are currently available)
+Note: no CuffFly or PasaFly (quite a few errors in the help file .. this is Parafly really) custom settings are currently available)
 * --path_reinforcement_distance <int>, minimum overlap of reads with growing transcript path (default: PE: 75, SE: 25). Set to 1 for the most lenient path extension requirements.
@@ Line 101: / Line 101: @@
 If, in a comparison between two alternative transcripts, they are found too similar, the transcript with the greatest cumulative compatible read (pair-path) support is retained, and the other is discarded.
-==  Butterfly Java and parallel execution settings ==
+==  Butterfly, Java and parallel execution settings ==
-* --bflyHeapSpaceMax <string>, java max heap space setting for butterfly (default: 4G this yields command
+* --bflyHeapSpaceMax <string>, java max heap space setting. Default is 4G. Actually this is just the java -Xmx option. '''4G''' causes '''java --Xmx4G'''.
- java -Xmx4G -jar Butterfly.jar ... $bfly_opts
+* --bflyHeapSpaceInit <string>, java initial heap space settings. Default: 1G. Actually the java '''-Xms''' option.
 * --bflyGCThreads <int>, threads for garbage collection (default: 2))
 * --bflyCPU <int>, CPUs to use (default will be normal number of CPUs; e.g., 2)

@@ Line 7: / Line 7: @@
 * Chrysalis (Contig Clustering & de Bruijn Graph Construction)
 * Butterfly (also called Parafly, referred to as Phase 2, assembling clusters of reads)
 This list follows the sequence of operations.

@@ Line 6: / Line 6: @@
 * Inchworm (Linear contig construction from k-mers)
 * Chrysalis (Contig Clustering & de Bruijn Graph Construction)
-* Butterfly (also called Parafly, referred to as Phase 2, assembling clusers of reads)
+* Butterfly (also called Parafly, referred to as Phase 2, assembling clusters of reads)
 This list follows the sequence of operations.

@@ Line 3: / Line 3: @@
 The widely established tool for transcriptome assembly. It consists of three main components (which is how it got its name) although a fourth one, Jellyfish, is also included in the following list because it's important, thogh not written by the Trinity team:
-* Jelly fish
+* Jelly fish (building a k-mer catalog from reads)
-* Inchworm
+* Inchworm (Linear contig construction from k-mers)
-* Chrysalis
+* Chrysalis (Contig Clustering & de Bruijn Graph Construction)
-* Butterfly
+* Butterfly (also called Parafly, referred to as Phase 2, assembling clusers of reads)
-This list follws the sequence of operations.
+This list follows the sequence of operations.
 = Version 2.3.2, full help file =
-This is an editted version. With the module loaded, type
+This is an edited version. With the module loaded, type
   Trinity --show-full-usage-info

@@ Line 63: / Line 63: @@
 == Chrysalis-related options ==
-#  --max_reads_per_graph <int>    :maximum number of reads to anchor within
+* --max_reads_per_graph <int>, maximum number of reads to anchor within a single graph (default: 200000)
-#                                  a single graph (default: 200000)
+* --min_glue <int>, min number of reads needed to glue two inchworm contigs together. (default: 2)
-#  --min_glue <int>               :min number of reads needed to glue two inchworm contigs
+* --no_bowtie, dont run bowtie to use pair info in chrysalis clustering.
-#                                  together. (default: 2)
+* --no_run_chrysalis, stop after running inchworm, before chrysalis. (phase 1, read clustering only)
 == Butterfly-related options ==

@@ Line 77: / Line 77: @@
   java -jar Butterfly.jar
 (note: only for expert or experimental use.  Commonly used parameters are exposed through this Trinity menu here).
-==  Butterfly read-pair grouping settings (used to define 'pair paths'):
+Butterfly default reconstruction mode settings
-#  Butterfly default reconstruction mode settings. (no CuffFly or PasaFly custom settings are currently available).
+Note: no CuffFly or PasaFly custom settings are currently available)
-−
-#  --path_reinforcement_distance <int>   :minimum overlap of reads with growing transcript
+* --path_reinforcement_distance <int>, minimum overlap of reads with growing transcript path (default: PE: 75, SE: 25). Set to 1 for the most lenient path extension requirements.
-#                                         path (default: PE: 75, SE: 25)
-#                                         Set to 1 for the most lenient path extension requirements.
+Butterfly transcript reduction settings:
-−
+* --no_path_merging, all final transcript candidates are output (including SNP variations, however, some SNPs may be unphased)
 ==  Butterfly Java and parallel execution settings ==
 * --bflyHeapSpaceMax <string>, java max heap space setting for butterfly (default: 4G this yields command
@@ Line 152: / Line 143: @@
 * see:
-/usr/local/Modules/modulefiles/tools/trinity/2.3.2/sample_data/test_Trinity_Assembly/
+ /usr/local/Modules/modulefiles/tools/trinity/2.3.2/sample_data/test_Trinity_Assembly/
 for sample data and 'runMe.sh' for example Trinity execution

@@ Line 125: / Line 125: @@
 == In silico Read Normalization Options ==
+* --normalize_max_read_cov <int>, defaults to 50
-#  --normalize_max_read_cov <int>       defaults to 50
+* --normalize_by_read_set, run normalization separate for each pair of fastq files, then one final normalization that combines the individual normalized reads. Consider using this if RAM limitations are a consideration.
 == Genome-guided de novo assembly ==
+* required: --genome_guided_max_intron <int>, maximum allowed intron length (also maximum fragment span on genome)
-#  * required:
+* optional: --genome_guided_min_coverage <int>, minimum read coverage for identifying and expressed region of the genome. (default: 1)
+* optional: --genome_guided_min_reads_per_partition <int>, default min of 10 reads per partition
 == Trinity phase 2 (parallel assembly of read clusters) Options ==
 * --grid_exec <string>, your command-line utility for submitting jobs to the grid. This should be a command line tool that accepts a single parameter:
-  ${your_submission_tool} /path/to/file/containing/commands.txt and this submission tool should exit(0) upon successful                                     completion of all commands.
+  ${your_submission_tool} /path/to/file/containing/commands.txt
 and this submission tool should exit(0) upon successful completion.
-#  --grid_node_CPU <int>                number of threads for each parallel process to leverage. (default: 1)
+* --grid_node_CPU <int>, number of threads for each parallel process to leverage. (default: 1)
+* --grid_node_max_memory <string>, max memory targeted for each grid node. (default: 1G)
-#  --grid_node_max_memory <string>         max memory targeted for each grid node. (default: 1G)
+Note: The '''--grid_node_CPU''' and '''--grid_node_max_memory''' are applied as the '''--CPU''' and '''--max_memory''' parameters for the Trinity jobs run in Trinity Phase 2 (assembly of read clusters).
-#            The --grid_node_CPU and --grid_node_max_memory are applied as
 == A typical Trinity command might be ==

@@ Line 26: / Line 26: @@
 Or,
-* --samples_file <string>         tab-delimited text file indicating biological replicate relationships.
+* --samples_file <string>         tab-delimited text file indicating biological replicate relationships. For example:
-== Misc ==
+  cond_A    cond_A_rep1    A_rep1_left.fq    A_rep1_right.fq
-* --SS_lib_type <string> Strand-specific RNA-Seq read orientation.
+  cond_A    cond_A_rep2    A_rep2_left.fq    A_rep2_right.fq
-#                                   if paired: RF or FR,
+  cond_B    cond_B_rep1    B_rep1_left.fq    B_rep1_right.fq
-#                                   if single: F or R.   (dUTP method = RF)
+  cond_B    cond_B_rep2    B_rep2_left.fq    B_rep2_right.fq
-#  --KMER_SIZE <int>               :kmer length to use (default: 25)  max=32
+== Misc ==
+* --SS_lib_type <string> Strand-specific RNA-Seq read orientation. If paired: RF or FR. If single: F or R. For dUTP method = RF.
-#  --prep                          :Only prepare files (high I/O usage) and stop before kmer counting.
+* --CPU <int>, number of CPUs to use, default: 2
+* --min_contig_length <int>, minimum assembled contig length to report  (default=200)
-#  --no_cleanup                    :retain all intermediate input files.
+* --long_reads <string>, fasta file containing error-corrected or circular consensus (CCS) pac bio reads (Note: experimental parameter, this functionality continues to be under development)
+* --genome_guided_bam <string>, genome guided mode, provide path to coordinate-sorted bam file (see genome-guided param section below)
-#  --no_version_check              :dont run a network check to determine if software updates are available.
+* --jaccard_clip, set if you have paired reads and you expect high gene density with UTR overlap (use FASTQ input file format for reads). Note that this is an expensive operation, so avoid using it unless necessary due to finding excessive fusion transcripts without it.)
+* --trimmomatic, run Trimmomatic to quality trim reads (see  option --quality_trimming_params).
 == Inchworm and K-mer counting-related options ==