Difference between revisions of "Bottlenose dolphin population genomic analysis"

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(Created page with "= Introduction = Used for population genetics studies. = Stages = == Quality trimming == Using trimmomatic")
 
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Using trimmomatic
 
Using trimmomatic
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 +
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}_${SLN1}_forward_paired.fq.gz # trimmed fq data file, forward paired reads
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TFQ2=${SSD2}/${SDN}/${SSD2}_${SRN2}_${SLN2}_reverse_paired.fq.gz # trimmed fq data file, reverse paired reads
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ACPTSZ=1000000 # acceptable size of a bam, a somewhat (only) risky way of seeing that it's OK.
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if [ -f $FQN1 ]; then
 +
    FQN1SZ=$( ls -l ${FQN1} | cut -d " " -f5 )
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else
 +
    FQN1SZ=0
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fi
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if [ -f $FQN2 ]; then
 +
    FQN2SZ=$( ls -l ${FQN2} | cut -d " " -f5 )
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else
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    FQN2SZ=0
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fi
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 +
if [[ "${FQN1SZ}" -lt "$ACPTSZ" ]] || [[ "${FQN2SZ}" -lt "$ACPTSZ" ]]; then
 +
    if [ -f $UBAM ]; then
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        UBSZ=$( ls -l ${UBAM} | cut -d " " -f5 )
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    else
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        UBSZ=0
 +
    fi
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    if [ "${UBSZ}" -lt "$ACPTSZ" ]; then
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        if [ -f $MTBAM ]; then
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            MBSZ=$( ls -l ${MTBAM} | cut -d " " -f5 )
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        else
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            MBSZ=0
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        fi
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        if [ "${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