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pre-processing_quality_control [2018/11/08 09:40]
david [Setting up]
pre-processing_quality_control [2018/11/08 10:46]
david [Running the programs through an sbatch script]
Line 257: Line 257:
 So let's look at one of ours: So let's look at one of ours:
 <​code>​ <​code>​
-$ head -4 01_input/SRR3567552_1.fastq ​+$ head -4 01_input/SRR3567551_1.fastq ​
 @SRR3567552.1 HISEQ:​222:​C3RTWACXX:​1:​1101:​1411:​2064 length=100 @SRR3567552.1 HISEQ:​222:​C3RTWACXX:​1:​1101:​1411:​2064 length=100
 GTGCTTGTGGACTGCTTGGTGGGGCTTGCTCTGCTAGGCGGACTACTTGCGTGCCTTGTTGTAGACGGCCTTGGTAGGTCTCTTGTAGACCGTCGCTTGC GTGCTTGTGGACTGCTTGGTGGGGCTTGCTCTGCTAGGCGGACTACTTGCGTGCCTTGTTGTAGACGGCCTTGGTAGGTCTCTTGTAGACCGTCGCTTGC
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 <​code>​ <​code>​
-$ ls -lh 01_input/SRR3567552_1.fastq ​+$ ls -lh 01_input/SRR3567551_1.fastq ​
 -rw-r--r-- 1 erinnish@colostate.edu erinnishgrp@colostate.edu 6.6G Oct 16 15:14 01_input/​SRR3567552_1.fastq -rw-r--r-- 1 erinnish@colostate.edu erinnishgrp@colostate.edu 6.6G Oct 16 15:14 01_input/​SRR3567552_1.fastq
 </​code>​ </​code>​
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 <​code>​ <​code>​
-$ sbatch 03_scripts/​number_of_reads.sbatch 01_input/SRR3567552_1.fastq+$ sbatch 03_scripts/​number_of_reads.sbatch 01_input/SRR3567551_1.fastq
 </​code>​ </​code>​
  
Line 328: Line 328:
 Summit was still recovering from maintenance yesterday, so my job just sat there, but I expect a file to be created in the directory called ''​numreads-1388630.out''​ containing the line: Summit was still recovering from maintenance yesterday, so my job just sat there, but I expect a file to be created in the directory called ''​numreads-1388630.out''​ containing the line:
 <​code>​ <​code>​
-01_input/SRR3567552_1.fastq has 20654219 reads.+01_input/SRR3567551_1.fastq has 20654219 reads.
 </​code>​ </​code>​
  
pre-processing_quality_control.txt ยท Last modified: 2018/11/08 10:46 by david