From 87204f7a538cf200d9335b9bbdb22b47774793fe Mon Sep 17 00:00:00 2001
From: Natasha Pavlovikj <npavlovikj2@unl.edu>
Date: Thu, 3 Feb 2022 11:22:01 -0600
Subject: [PATCH] Update scythe documentation
---
.../bioinformatics_tools/pre_processing_tools/scythe.md | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/scythe.md b/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/scythe.md
index f19e2bb0..f24854a5 100644
--- a/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/scythe.md
+++ b/content/applications/app_specific/bioinformatics_tools/pre_processing_tools/scythe.md
@@ -14,7 +14,7 @@ $ scythe -a adapter_file.fasta input_reads.fastq -o output_reads.fastq
{{< /highlight >}}
where **adapter_file.fasta** is fasta input file of the adapter sequences that need to be removed from the 3' end of the sequence data, and **input_reads.fastq** is the input sequencing data in fastq format.
-The file **output_reads.fastq** contains the sequencing reads with removed adapters. If the adapter sequences are unknown, Scythe by itself provides two adapter sequences that can be used with the **-a** option: **illumina_adapters.fa** and **truseq_adapters.fasta**.
+The file **output_reads.fastq** contains the sequencing reads with removed adapters. If the adapter sequences are unknown, Scythe by itself provides Illumina adapter sequences that can be used with the **-a** option: **illumina_adapters.fa**.
More information about Scythe can found by typing:
{{< highlight bash >}}
@@ -36,13 +36,13 @@ Simple Scythe script that uses the `illumina_adapters.fa` file and `input_reads.
module load scythe/0.991
-scythe -a ${SCYTHE_HOME}/illumina_adapters.fa input_reads.fastq -o output_reads.fastq
+scythe -a ${SCYTHE_ADAPTERS}/illumina_adapters.fa input_reads.fastq -o output_reads.fastq
{{< /highlight >}}
{{% /panel %}}
Scythe is single threaded program, and therefore both `#SBATCH --nodes` and `#SBATCH --ntasks-per-node` are set to **1**.
-The two adapter sequences provided by Scythe are stored in **$SCYTHE_HOME**. Hence, to access the illumina adapter file use: `$SCYTHE_HOME/illumina_adapters.fa`, and to access the TruSeq file use: `$SCYTHE_HOME/truseq_adapters.fasta`.
+The Illumina adapter sequences provided by Scythe are stored in **$SCYTHE_ADAPTERS**. Hence, to access the illumina adapter file use: `$SCYTHE_ADAPTERS/illumina_adapters.fa`.
### Scythe Output
--
GitLab