From d3e2c88b4a2a46f86c57a31b566f8ef781f3ca85 Mon Sep 17 00:00:00 2001
From: Natasha Pavlovikj <natasha.pavlovikj@huskers.unl.edu>
Date: Wed, 1 Jul 2020 03:49:49 +0000
Subject: [PATCH] Fix doc for Trinity
---
.../de_novo_assembly_tools/trinity/_index.md | 10 +++++-----
.../trinity/running_trinity_in_multiple_steps.md | 14 +++++++-------
2 files changed, 12 insertions(+), 12 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 59165f19..6e19c01b 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
@@ -5,7 +5,7 @@ weight = "52"
+++
-[Trinity](https://github.com/trinityrnaseq/trinityrnaseq/wiki) is a method for efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: `Inchworm`, `Chrysalis`, and `Butterfly`. All these modules can be applied sequentially to process large RNA-Seq datasets.
+[Trinity](https://github.com/trinityrnaseq/trinityrnaseq/wiki) is a method for efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines four independent software modules: `Normalization`, `Inchworm`, `Chrysalis` and `Assembly`. All these modules can be applied sequentially to process large RNA-Seq datasets.
The basic usage of Trinity is:
@@ -24,25 +24,25 @@ Running the Trinity pipeline from beginning to end on large datasets may exceed
{{% panel theme="info" header="Step 1 Options" %}}
{{< highlight bash >}}
-Trinity.pl [options] --no_run_chrysalis
+Trinity [options] --no_run_inchworm
{{< /highlight >}}
{{% /panel %}}
{{% panel theme="info" header="Step 2 Options" %}}
{{< highlight bash >}}
-Trinity.pl [options] --no_run_quantifygraph
+Trinity [options] --no_run_chrysalis
{{< /highlight >}}
{{% /panel %}}
{{% panel theme="info" header="Step 3 Options" %}}
{{< highlight bash >}}
-Trinity.pl [options] --no_run_butterfly
+Trinity [options] --no_distributed_trinity_exec
{{< /highlight >}}
{{% /panel %}}
{{% panel theme="info" header="Step 4 Options" %}}
{{< highlight bash >}}
-Trinity.pl [options]
+Trinity [options]
{{< /highlight >}}
{{% /panel %}}
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 5bce95bb..086a9ed4 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
@@ -7,7 +7,7 @@ weight = "10"
## Running Trinity with Paired-End fastq data with 8 CPUs and 100GB of RAM
-The first step of running Trinity is to run Trinity with the option **--no_run_chrysalis**:
+The first step of running Trinity is to run Trinity with the option **--no_run_inchworm**:
{{% panel header="`trinity_step1.submit`"%}}
{{< highlight bash >}}
#!/bin/sh
@@ -21,12 +21,12 @@ The first step of running Trinity is to run Trinity with the option **--no_run_c
module load trinity
-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
+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_inchworm
{{< /highlight >}}
{{% /panel %}}
-The second step of running Trinity is to run Trinity with the option **--no_run_quantifygraph**:
+The second step of running Trinity is to run Trinity with the option **--no_run_chrysalis**:
{{% panel header="`trinity_step2.submit`"%}}
{{< highlight bash >}}
#!/bin/sh
@@ -40,12 +40,12 @@ The second step of running Trinity is to run Trinity with the option **--no_run_
module load trinity
-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
+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 %}}
-The third step of running Trinity is to run Trinity with the option **--no_run_butterfly**:
+The third step of running Trinity is to run Trinity with the option **--no_distributed_trinity_exec**:
{{% panel header="`trinity_step3.submit`"%}}
{{< highlight bash >}}
#!/bin/sh
@@ -59,7 +59,7 @@ The third step of running Trinity is to run Trinity with the option **--no_run_b
module load trinity
-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
+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_distributed_trinity_exec
{{< /highlight >}}
{{% /panel %}}
@@ -89,5 +89,5 @@ Trinity outputs number of files in its `trinity_out/` output directory after eac
{{% notice tip %}}
-The Inchworm (step 1) and Chrysalis (step 2) steps can be memory intensive. A basic recommendation is to have **1GB of RAM per 1M ~76 base Illumina paired-end reads**.
+The Inchworm (step 2) and Chrysalis (step 3) steps can be memory intensive. A basic recommendation is to have **1GB of RAM per 1M ~76 base Illumina paired-end reads**.
{{% /notice %}}
--
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