...
We're going to copy all of these into a new directory called IGV to make it easier to just transfer the ones that we want. Change into your intro_to_mapping directory and run these commands if you just came from mapping:
| Code Block |
|---|
mkdir IGV
cp NC_012967.1.gbk.gff IGV
cp bowtie/bowtie.sam IGV/bowtie.sam
cp bowtie2/bowtie2.sam IGV/bowtie2.sam
cp bwa/SRR030257.sam IGV/bwa.sam
|
| Expand |
|---|
| If you just came from variant calling, you can run these instead... |
|---|
| If you just came from variant calling, you can run these instead... |
|---|
|
Add these: | Code Block |
|---|
mkdir IGV
cp NC_012967.1.gbk.gff IGV
cp samtools_bowtie/NC_012967.1.fasta IGV
cp samtools_bowtie/NC_012967.1.fasta.fai IGV
cp samtools_bowtie2/SRR030257.sorted.bam IGV/bowtie2.sorted.bam
cp samtools_bowtie2/SRR030257.sorted.bam.bai IGV/bowtie2.sorted.bam.bai
cp samtools_bowtie/SRR030257.sorted.bam IGV/bowtie.sorted.bam
cp samtools_bowtie/SRR030257.sorted.bam.bai IGV/bowtie.sorted.bam.bai
cp samtools_bwa/SRR030257.sorted.bam IGV/bwa.sorted.bam
cp samtools_bwa/SRR030257.sorted.bam.bai IGV/bwa.sorted.bam.bai
cp comparison/* IGV
|
|
Now, copy this entire IGV directory back to your local Desktop machine.
...