From 85a2048246e342e6db05a54649f7681868a70176 Mon Sep 17 00:00:00 2001 From: Meeta Mistry Date: Wed, 22 May 2024 15:54:48 -0400 Subject: [PATCH] Update 04_alignment_file_processing.md --- lessons/04_alignment_file_processing.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/lessons/04_alignment_file_processing.md b/lessons/04_alignment_file_processing.md index ceb20e2..38709a4 100644 --- a/lessons/04_alignment_file_processing.md +++ b/lessons/04_alignment_file_processing.md @@ -230,7 +230,7 @@ The components of this command are: * `--SORT_ORDER coordinate` Sort the output file by **coordinates** * `--CREATE_INDEX true` Setting the `CREATE_INDEX` equal to `true` will create an index of the final BAM output. The index creation can also be accomplished by using the `BuildBamIndex` command within `Picard`, but this `CREATE_INDEX` functionality is built into many `Picard` functions, so you can often use it at the last stage of processing your BAM file to save having to run `BuildBamIndex` after. -Now this script is all set to run! Go ahead and save and quit. +Go ahead and save and quit. **Don't run it just yet!**
Click here to see what our final sbatchcode script for the normal sample should look like @@ -658,6 +658,8 @@ squeue -u $USER sbatch picard_alignment_processing_normal.sbatch sbatch picard_alignment_processing_tumor.sbatch ``` + +> **NOTE:** These scripts will take ~2 hours for each to run! [Next Lesson >>](05_alignment_QC.md)