Update fastq_to_bam.rst

docs/source/fastq_to_bam.rst

@@ -28,9 +28,6 @@ From fastq to final valid pairs bam file
       bwa mem -5SP -T0 -t16 hg38.fasta OmniC_2M_R1.fastq OmniC_2M_R2.fastq| pairtools parse --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --nproc-in 8 --nproc-out 8 --chroms-path hg38.genome | pairtools sort --tmpdir=/home/ubuntu/ebs/temp/ --nproc 16|pairtools dedup --nproc-in 8 --nproc-out 8 --mark-dups --output-stats stats.txt|pairtools split --nproc-in 8 --nproc-out 8 --output-pairs mapped.pairs --output-sam -|samtools view -bS -@16 | samtools sort -@16 -o mapped.PT.bam;samtools index mapped.PT.bam
 
 
-|clock| The full command above, with 2M read pairs on an Ubuntu 18.04 machine with 16 CPUs and 64GiB was completed in less than 5 minutes.
-On the same machine type.
-
 |clock| The full command above, with 2M read pairs on an Ubuntu 18.04 machine with 16 CPUs and 64GiB was completed in less than 5 minutes. 
 On the same machine type.
 
@@ -253,4 +250,4 @@ Index the bam file:
 The `mapped.PT.bam` is the final bam file that will be used downstream steps.
 
 
-The above steps resulted in multiple intermediate files, to simplify the process and avoid intermediate files, you can pipe the steps as in the example above (:ref: `fastq to final valid pairs bam file - for the impatient <impatient>`)
+The above steps resulted in multiple intermediate files, to simplify the process and avoid intermediate files, you can pipe the steps as in the example above (:ref: `fastq to final valid pairs bam file - for the impatient <impatient>`)