Bottlenose dolphin population genomic analysis

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. 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

   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 ${MTBAM} | cut -d " " -f5 )
       else
           MBSZ=0
       fi
       if [ "${MBSZ}" -lt "$ACPTSZ" ]; then
           if [ -f $MTSAM ]; then
               MSSZ=$( ls -l ${MTSAM} | cut -d " " -f5 )
           else
               MSSZ=0
           fi