@@ -25,7 +25,7 @@ where **index_prefix** is the index for the reference genome generated from **bw
Simple SLURM script for running **bwa mem** on Crane with paired-end fastq input data, `index_prefix` as reference genome index, SAM output file and `8 CPUs` is shown below:
@@ -30,7 +30,7 @@ Prior running TopHat/TopHat2, an index from the reference genome should be built
An example of how to run TopHat2 on Crane with paired-end fastq files `input_reads_pair_1.fastq` and `input_reads_pair_2.fastq`, reference index `index_prefix` and `8 CPUs` is shown below:
An example of how to run Bowtie2 local alignment on Crane utilizing the default Horse, *Equus caballus* index (*BOWTIE2\_HORSE*) with paired-end fasta files and 8 CPUs is shown below:
@@ -17,7 +17,7 @@ where **input_alignments.[bam|sam]** is the input file with the alignments in BA
Running **samtools view** on Crane with `8 CPUs`, input file `input_alignments.sam` with available header (**-S**), output in BAM format (**-b**) and output file `output_alignments.bam` is shown below: