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--- trinity_for_assembling_transcript_reads [2018/06/28 15:35] – 134.190.133.209
+++ trinity_for_assembling_transcript_reads [2025/11/07 11:27] (current) – 134.190.191.186
@@ Line 1: / Line 1: @@
 ====== Trinity - Assembly of transcriptome reads ======
-Documentation by Shelby Williams
+Documentation by Shelby Williams (last updated by D. Salas-Leiva, 01-07-2020 and J. Martijn 24-04-2023 and K.Dunn 07-11-2025)
 Trinity is an assembler of RNA-seq reads, after they have been trimmed. Trinity uses three programs (Inchworm, Chrysalis, and Butterfly) to assemble large volumes of transcriptome reads. The output of Trinity is the Trinity.fasta file found in the /trinity_out_dir/ folder/
 ----
 A simple Trinity shell script, using the new conda-environments:
+**For strand-specific data (No genome guided or //de novo//):  **
+It could be **RF** or **FR**. We usually get RF (typical of the dUTP/UDG sequencing method). If unsure, you need to draw violin plots to determine the specificity.
 <code>
 #!/bin/bash
@@ Line 14: / Line 18: @@
 #$ -cwd
 #$ -pe threaded 10
-#$ -q 256G-batch
-source activate trinity
+##source activate trinity-2.11-with-workaround no longer need to use, use newest version instead
-Trinity --seqType fq --left RetortaCarp_1_PairNtrim.fastq --right RetortaCarp_2_PairNtrim.fastq --CPU 10 --max_memory 20G
+## this special built is version is 2.11 - use new version now instead see below
+source activate trinity
+## this is version 2.15.2
+Trinity \
+    --seqType fq \
+    --SS_lib_type RF \
+    --left Reads_R1_PairNtrim.fastq \
+    --right Reads_2_PairNtrim.fastq \
+    --CPU 10 \
+    --max_memory 20G
+conda deactivate
+</code>
+If your genome is compact, that is, genes are very close together with minimum intergenic space, it may be beneficial to run Trinity with the ''--jaccard_clip'' option. This can prevent Trinity from falsely assembling transcripts from multiple consecutive genes in a row into a single transcript.
+From the ''--help'' :
+<code>
+#  --jaccard_clip                  :option, set if you have paired reads and
+#                                   you expect high gene density with UTR
+#                                   overlap (use FASTQ input file format
+#                                   for reads).
+#                                   (note: jaccard_clip is an expensive
+#                                   operation, so avoid using it unless
+#                                   necessary due to finding excessive fusion
+#                                   transcripts w/o it.)
+</code>
+**For strand-specific data (Genome guided):  **
+It could be **RF** or **FR**. We usually get RF (typical of the dUTP/UDG sequencing method). If unsure, you need to draw violin plots to determine the specificity.
+<code>
+#!/bin/bash
+#$ -S /bin/bash
+. /etc/profile
+#$ -cwd
+#$ -pe threaded 10
+source activate trinity-2.11-with-workaround
+# this special built is version is 2.11
+Trinity \
+    --CPU 10 \
+    --max_memory 100G \
+    --genome_guided_bam yourgenome.fasta.sambamsorted.bam \
+    --genome_guided_max_intron 1000 \
+    --SS_lib_type RF
+    -
+conda deactivate
+</code>
+**For NO strand specific data:**
+<code>
+#!/bin/bash
+#$ -S /bin/bash
+. /etc/profile
+#$ -cwd
+#$ -pe threaded 10
+source activate trinity-2.11-with-workaround
+# this special built is version is 2.11
+Trinity \
+    --seqType fq \
+    --left Reads_R1_PairNtrim.fastq \
+    --right Reads_2_PairNtrim.fastq \
+    --CPU 10 \
+    --max_memory 20G
 source deactivate
 </code>
-#Note: this should always invoke the latest version of Trinity installed on perun. You can check this by looking at the output file or invoking Trinity directly from the prompt with Trinity --version.
 **ATTENTION!**
-Trinity 2.4.0 is not compatible with Bowtie2. Skip this step by adding the flag **--no_bowtie**
+Some Trinity  versions, such as 2.4.0, are not compatible with Bowtie2. Skip this step by adding the flag **--no_bowtie**