Difference between revisions of "Bottlenose dolphin population genomic analysis"
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TFQ2=${SSD2}/${SDN}/${SSD2}_${SRN2}_${SLN2}_reverse_paired.fq.gz # trimmed fq data file, reverse paired reads | TFQ2=${SSD2}/${SDN}/${SSD2}_${SRN2}_${SLN2}_reverse_paired.fq.gz # trimmed fq data file, reverse paired reads | ||
ACPTSZ=1000000 # acceptable size of a bam, a somewhat (only) risky way of seeing that it's OK. | ACPTSZ=1000000 # acceptable size of a bam, a somewhat (only) risky way of seeing that it's OK. | ||
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− | + | bwa mem -t $NSLOTS $MITOREFLOC $TFQ1 $TFQ2 > $MTSAM | |
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Revision as of 23:58, 30 December 2016
Introduction
Used for population genetics studies.
Stages
Quality trimming
Using trimmomatic
MITOREFLOC=/storage/home/users/ml228/Genomics/NEA_BGI_data_ALL/NEA_BGI_clean_raw_data/Refs/mitogenome/gi_557468684_gb_KF570351.1_.fasta
- FQN1, the forward paired output from Trimmomatic
- FQN2, the reverse paired output from Trimmomatic
- UBAM, the unmapped bam reflecting exclusion of mitochondiral mappings
MTBAM=${SSD1}/${MDN}/${SSD1}_${SRN1}_${SLN1}_to_mt_sorted.bam # the alignment to mito, sorted and now in bam format. MTSAM=${SSD1}/${MDN}/mito_aln-pe${SSD1}_${SRN1}_${SLN1}.sam # the raw sam alignment to mito, unsorted TFQ1=${SSD1}/${SDN}/${SSD1}_${SRN1}_${SLN1}_forward_paired.fq.gz # trimmed fq data file, forward paired reads TFQ2=${SSD2}/${SDN}/${SSD2}_${SRN2}_${SLN2}_reverse_paired.fq.gz # trimmed fq data file, reverse paired reads ACPTSZ=1000000 # acceptable size of a bam, a somewhat (only) risky way of seeing that it's OK.
bwa mem -t $NSLOTS $MITOREFLOC $TFQ1 $TFQ2 > $MTSAM