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Revision as of 11:34, 18 May 2015
, 11:34, 18 May 2015no edit summary
** Using ~/ means the command will work even if you have changed directories
** Using ~/ means the command will work even if you have changed directories
You will see 2 files:
You will see 2 or more files (if you have multiple pairs):
* Sample#_R1.fastq.gz - 1st in pair
* *Sample#_*_R1.fastq.gz - 1st in pair
* Sample#_R2.fastq.gz - 2nd in pair
* *Sample#_*_R2.fastq.gz - 2nd in pair
== What did I do to run the alignment? ==
== What did I do to run the alignment? ==
SAMPLE FASTQ1 FASTQ2
SAMPLE FASTQ1 FASTQ2
Sample# /path/to/Sample#/fastqs/Sample#_R1.fastq.gz /path/to/Sample#/fastqs/Sample#_R2.fastq.gz
Sample# /path/to/Sample#/fastqs/*Sample#_*_R1.fastq.gz /path/to/Sample#/fastqs/*Sample#_*_R2.fastq.gz
You can see what your fastq.list looks like
You can see what your fastq.list looks like
* What changes from the default settings did I make?
* What changes from the default settings did I make?
*# Use multiple BWA_THREADS
*# Use multiple BWA_THREADS
*# Set FASTQ_LIST
*# Set FASTQ_LIST
** various number of BWA_THREADS for each sample
** various number of BWA_THREADS for each sample
** full paths to:
** full paths to:
*** FASTQ_LIST (and I sometimes had multiple samples in 1 list - but each gets aligned independently)
*** FASTQ_LIST
*** OUT_DIR
*** OUT_DIR
cat ~/Sample*/gotcloud.conf
cat ~/Sample*/gotcloud.conf
