From c0ecff14c560bbb973a2f6fb289505d008901e98 Mon Sep 17 00:00:00 2001 From: Muhammad Elhossary Date: Sun, 7 Apr 2024 17:11:27 +0200 Subject: [PATCH 1/2] fix for example align command --- docs/source/example_analysis.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/example_analysis.rst b/docs/source/example_analysis.rst index 1ef598b..3b9f755 100644 --- a/docs/source/example_analysis.rst +++ b/docs/source/example_analysis.rst @@ -141,7 +141,7 @@ tell READemption to use 4 CPU (``-p 4``) and perform a poly-A-clipping :: - $ reademption align -p 4 --poly_a_clipping --project_path READemption_analysis + $ reademption align -p 4 --poly_a_clipping --fastq --progress --project_path READemption_analysis Once this the mapping is done the file ``read_alignment_stats.csv`` is created which can be found in From 1ffff97dfe359b17b82a586f34e417a7ce55fbe8 Mon Sep 17 00:00:00 2001 From: Muhammad Elhossary Date: Sun, 7 Apr 2024 17:15:44 +0200 Subject: [PATCH 2/2] fix the example align command As fastq reads were used, --fastq argument should be enabled Also, --progress shows useful information, if the command crashes, you can know when and where it happened --- docs/source/example_analysis.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/example_analysis.rst b/docs/source/example_analysis.rst index 3b9f755..5f9e0a2 100644 --- a/docs/source/example_analysis.rst +++ b/docs/source/example_analysis.rst @@ -400,7 +400,7 @@ tell READemption to use 4 CPU (``-p 4``) and perform a poly-A-clipping :: - $ reademption align -p 4 --poly_a_clipping --project_path READemption_analysis + $ reademption align -p 4 --poly_a_clipping --fastq --progress --project_path READemption_analysis Once this the mapping is done the file ``read_alignment_stats.csv`` is created which can be found in