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68 bytes removed
, 11:34, 18 May 2015
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| ** Using ~/ means the command will work even if you have changed directories | | ** Using ~/ means the command will work even if you have changed directories |
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− | 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 |
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| == What did I do to run the alignment? == | | == What did I do to run the alignment? == |
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| 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 |
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| * What changes from the default settings did I make? | | * What changes from the default settings did I make? |
− | *# Use BWA instead of BWA_MEM
| |
| *# Use multiple BWA_THREADS | | *# Use multiple BWA_THREADS |
| *# Set FASTQ_LIST | | *# Set FASTQ_LIST |
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| ** 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 |