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.
−
if [ -f $FQN1 ]; then
 
−
    FQN1SZ=$( ls -l ${FQN1} | cut -d " " -f5 )
 
−
else
 
−
    FQN1SZ=0
 
−
fi
 
−
if [ -f $FQN2 ]; then
 
−
    FQN2SZ=$( ls -l ${FQN2} | cut -d " " -f5 )
 
−
else
 
−
    FQN2SZ=0
 
−
fi
 
  
−
if [[ "${FQN1SZ}" -lt "$ACPTSZ" ]] || [[ "${FQN2SZ}" -lt "$ACPTSZ" ]]; then
+
bwa mem -t $NSLOTS $MITOREFLOC $TFQ1 $TFQ2 > $MTSAM
−
    if [ -f $UBAM ]; then
 
−
        UBSZ=$( ls -l ${UBAM} | cut -d " " -f5 )
 
−
    else
 
−
        UBSZ=0
 
−
    fi
 
−
    if [ "${UBSZ}" -lt "$ACPTSZ" ]; then
 
−
        if [ -f $MTBAM ]; then
 
−
            MBSZ=$( ls -l ${MTBAM} | cut -d " " -f5 )
 
−
        else
 
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            MBSZ=0
 
−
        fi
 
−
        if [ "${MBSZ}" -lt "$ACPTSZ" ]; then
 
−
            if [ -f $MTSAM ]; then
 
−
                MSSZ=$( ls -l ${MTSAM} | cut -d " " -f5 )
 
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            else
 
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                MSSZ=0
 
−
            fi
 

Revision as of 00:58, 31 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
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