Difference between revisions of "Bottlenose dolphin population genomic analysis"
(Created page with "= Introduction = Used for population genetics studies. = Stages = == Quality trimming == Using trimmomatic") |
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Using trimmomatic | 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 ${MTSAM} | cut -d " " -f5 ) | ||
| + | else | ||
| + | MSSZ=0 | ||
| + | fi | ||
Revision as of 23:57, 30 December 2016
Introduction
Used for population genetics studies.
Stages
Quality trimming
Using trimmomatic
MITOREFLOC=/storage/home/users/ml228/Genomics/NEA_BGI_data_ALL/NEA_BGI_clean_raw_data/Refs/mitogenome/gi_557468684_gb_KF570351.1_.fasta
- FQN1, the forward paired output from Trimmomatic
- FQN2, the reverse paired output from Trimmomatic
- UBAM, the unmapped bam reflecting exclusion of mitochondiral mappings
MTBAM=${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. 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
