From 3c09e1a280b0bdac5f626b6a36411a18f9b8054c Mon Sep 17 00:00:00 2001
From: Natasha Pavlovikj <npavlovikj2@unl.edu>
Date: Mon, 29 Jun 2020 18:08:24 -0500
Subject: [PATCH] Update Trinity version and command
---
.../de_novo_assembly_tools/trinity/_index.md | 4 ++--
.../trinity/running_trinity_in_multiple_steps.md | 16 ++++++++--------
2 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/_index.md b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/_index.md
index 09067c00..59165f19 100644
--- a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/_index.md
+++ b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/_index.md
@@ -10,9 +10,9 @@ weight = "52"
The basic usage of Trinity is:
{{< highlight bash >}}
-$ Trinity --seqType [fa|fq] --JM <jellyfish_memory> --left input_reads_pair_1.[fa|fq] --right input_reads_pair_2.[fa|fq] [options]
+$ Trinity --seqType [fa|fq] --max_memory <maximum_memory> --left input_reads_pair_1.[fa|fq] --right input_reads_pair_2.[fa|fq] [options]
{{< /highlight >}}
-where **input_reads_pair_1.[fa|fq]** and **input_reads_pair_2.[fa|fq]** are the input paired-end files of sequence reads in fasta/fastq format, and **--seqType** is the type of these input reads. The option **--JM** defines the number of GB of system memory required for k-mer counting by jellyfish.
+where **input_reads_pair_1.[fa|fq]** and **input_reads_pair_2.[fa|fq]** are the input paired-end files of sequence reads in fasta/fastq format, and **--seqType** is the type of these input reads. The option **--max_memory** specifies the maximum memory to use with Trinity.
Additional Trinity **options** can be found in the Trinity website, or by typing:
{{< highlight bash >}}
diff --git a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md
index 8caa894f..5bce95bb 100644
--- a/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md
+++ b/content/applications/app_specific/bioinformatics_tools/de_novo_assembly_tools/trinity/running_trinity_in_multiple_steps.md
@@ -19,9 +19,9 @@ The first step of running Trinity is to run Trinity with the option **--no_run_c
#SBATCH --output=Trinity_Step1.%J.out
#SBATCH --error=Trinity_Step1.%J.err
-module load trinity/2.6
+module load trinity
-Trinity --seqType fq --JM 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_chrysalis
+Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_chrysalis
{{< /highlight >}}
{{% /panel %}}
@@ -38,9 +38,9 @@ The second step of running Trinity is to run Trinity with the option **--no_run_
#SBATCH --output=Trinity_Step2.%J.out
#SBATCH --error=Trinity_Step2.%J.err
-module load trinity/2.6
+module load trinity
-Trinity --seqType fq --JM 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_quantifygraph
+Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_quantifygraph
{{< /highlight >}}
{{% /panel %}}
@@ -57,9 +57,9 @@ The third step of running Trinity is to run Trinity with the option **--no_run_b
#SBATCH --output=Trinity_Step3.%J.out
#SBATCH --error=Trinity_Step3.%J.err
-module load trinity/2.6
+module load trinity
-Trinity --seqType fq --JM 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_butterfly
+Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE --no_run_butterfly
{{< /highlight >}}
{{% /panel %}}
@@ -76,9 +76,9 @@ The fourth step of running Trinity is to run Trinity without any additional opti
#SBATCH --output=Trinity_Step4.%J.out
#SBATCH --error=Trinity_Step4.%J.err
-module load trinity/2.6
+module load trinity
-Trinity --seqType fq --JM 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE
+Trinity --seqType fq --max_memory 100G --left input_reads_pair_1.fastq --right input_reads_pair_2.fastq --SS_lib_type FR --output trinity_out/ --CPU $SLURM_NTASKS_PER_NODE
{{< /highlight >}}
{{% /panel %}}
--
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