Commit 3c09e1a2 authored by Natasha Pavlovikj's avatar Natasha Pavlovikj

Update Trinity version and command

parent dc04cbd7
......@@ -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 >}}
......
......@@ -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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