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pre-processing_quality_control [2018/11/08 09:38]
david [A great get from git]
pre-processing_quality_control [2018/11/08 10:46] (current)
david [Running the programs through an sbatch script]
Line 90: Line 90:
  2 files changed, 13 insertions(+),​ 9 deletions(-)  2 files changed, 13 insertions(+),​ 9 deletions(-)
 </​code>​ </​code>​
 +
 +Check that everything is OK.
 +
 +<​code>​
 +$ make setup
 +</​code>​
 +
 <​code>​ <​code>​
 $ ls $ ls
Line 250: 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
Line 262: Line 269:
  
 <​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>​
Line 280: Line 287:
  
 <​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 321: 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.1541695120.txt.gz ยท Last modified: 2018/11/08 09:38 by david