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Update FRiP calculation (account for paired-end samples) #2

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Update FRiP calculation (account for paired-end samples) #2

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46 changes: 34 additions & 12 deletions bin/pipeline.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -756,10 +756,10 @@ if [ $DEBUG_TXT == 1 ]; then
# modified by kyra; forward/reverse strands represented as distinct lines in temp_NRF_PBC_file
# therefore, must divide uniqgenomepos by two for paired-end read fastq file input
if [ -z "$FASTQ2" ]; then
echo "single-end read fastq file is provided as input, divide uniqgenomepos by 2"
echo "single-end read fastq file is provided as input, no modification needed"
uniqgenomepos=`cat $temp_NRF_PBC_file | wc -l`
else
echo "paired-end read fastq file is provided as input, no modification needed"
echo "paired-end read fastq file is provided as input, divide uniqgenomepos by 2"
uniqgenomepos=$(( $(cat $temp_NRF_PBC_file | wc -l) / 2 ))
fi

Expand All @@ -772,7 +772,13 @@ if [ $DEBUG_TXT == 1 ]; then

# number of genomic locations where exactly one read maps uniquely
echo "# number of genomic locations where exactly one read maps uniquely"
M1=`awk '$4==1' $temp_NRF_PBC_file | wc -l`
if [ -z "$FASTQ2" ]; then
echo "single-end read fastq file is provided as input, no modification needed"
M1=`awk '$4==1' $temp_NRF_PBC_file | wc -l`
else
echo "paired-end read fastq file is provided as input, divide M1 by 2"
M1=$(( $(awk '$4==1' $temp_NRF_PBC_file | wc -l) / 2 ))
fi

# PCR Bottlenecking Coefficient 1 (PBC1) is computed by considering the
# number of genomic locations where exactly one read maps uniquely
Expand All @@ -782,7 +788,13 @@ if [ $DEBUG_TXT == 1 ]; then

# number of genomic locations where exactly two reads map uniquely
echo "# number of genomic locations where exactly two reads map uniquely"
M2=`awk '$4==2' $temp_NRF_PBC_file | wc -l`
if [ -z "$FASTQ2" ]; then
echo "single-end read fastq file is provided as input, no modification needed"
M2=`awk '$4==2' $temp_NRF_PBC_file | wc -l`
else
echo "paired-end read fastq file is provided as input, divide M2 by 2"
M2=$(( $(awk '$4==2' $temp_NRF_PBC_file | wc -l) / 2 ))
fi

# PCR Bottlenecking Coefficient 2 (PBC2)
# ratio of the following quantities
Expand Down Expand Up @@ -1120,12 +1132,14 @@ if [ $DEBUG_TXT == 1 ]; then
if [[ ! -f $FRiP_outfile || $Overwrite == 1 ]]; then
# number of reads within MACS2 narrow peaks (q threshold = 0.05)
echo "# number of reads within MACS2 narrow peaks (q threshold = 0.05)"
macs2_nreads_narrowpeak=`samtools view -cL $QFilt1File $bowtie2_BAM_prefix'.rmdup.bam'`
#macs2_nreads_narrowpeak=`samtools view -cL $QFilt1File $bowtie2_BAM_prefix'.rmdup.bam'`
macs2_nreads_narrowpeak=`samtools view -L $QFilt1File $bowtie2_BAM_prefix'.rmdup.bam' | cut -f1 | sort -k1,1 | uniq | wc -l` # edited by Kyra, account for paired-end
FRiP_narrowpeak=`bc <<< "scale=3; ($macs2_nreads_narrowpeak * 1.0) / $uniq_mapped_read"`

# number of reads within MACS2 broad peaks (q threshold = 0.05)
echo "# number of reads within MACS2 broad peaks (q threshold = 0.05)"
macs2_nreads_broadpeak=`samtools view -cL $QFilt1FileBroad $bowtie2_BAM_prefix'.rmdup.bam'`
#macs2_nreads_broadpeak=`samtools view -cL $QFilt1FileBroad $bowtie2_BAM_prefix'.rmdup.bam'`
macs2_nreads_broadpeak=`samtools view -L $QFilt1FileBroad $bowtie2_BAM_prefix'.rmdup.bam' | cut -f1 | sort -k1,1 | uniq | wc -l` # edited by Kyra, account for paired-end
FRiP_broadpeak=`bc <<< "scale=3; ($macs2_nreads_broadpeak * 1.0) / $uniq_mapped_read"`

echo -e 'UniqMappedRead\tMappedReadNarrowpeak\tFRiPNarrowPeak\tMappedReadBroadpeak\tFRiPBroadPeak' > $FRiP_outfile
Expand Down Expand Up @@ -1362,12 +1376,16 @@ if [ $DEBUG_TXT == 1 ]; then
if [[ ! -f $FRiP_outfile || $Overwrite == 1 ]]; then
# number of reads within MACS2 narrow peaks (q threshold = 0.05)
echo "# number of reads within MACS2 narrow peaks (q threshold = 0.05)"
macs2_nreads_narrowpeak=`samtools view -cL $QFilt1File $bowtie2_BAM_prefix'.rmdup.bam'`
#macs2_nreads_narrowpeak=`samtools view -cL $QFilt1File $bowtie2_BAM_prefix'.rmdup.bam'`
macs2_nreads_narrowpeak=`samtools view -L $QFilt1File $bowtie2_BAM_prefix'.rmdup.bam' | cut -f1 | sort -k1,1 | uniq | wc -l` # edited by Kyra, account for paired-end

FRiP_narrowpeak=`bc <<< "scale=3; ($macs2_nreads_narrowpeak * 1.0) / $uniq_mapped_read"`

# number of reads within MACS2 broad peaks (q threshold = 0.05)
echo "# number of reads within MACS2 broad peaks (q threshold = 0.05)"
macs2_nreads_broadpeak=`samtools view -cL $QFilt1FileBroad $bowtie2_BAM_prefix'.rmdup.bam'`
#macs2_nreads_broadpeak=`samtools view -cL $QFilt1FileBroad $bowtie2_BAM_prefix'.rmdup.bam'`
macs2_nreads_broadpeak=`samtools view -L $QFilt1FileBroad $bowtie2_BAM_prefix'.rmdup.bam' | cut -f1 | sort -k1,1 | uniq | wc -l` # edited by Kyra, account for paired-end

FRiP_broadpeak=`bc <<< "scale=3; ($macs2_nreads_broadpeak * 1.0) / $uniq_mapped_read"`

echo -e 'UniqMappedRead\tMappedReadNarrowpeak\tFRiPNarrowPeak\tMappedReadBroadpeak\tFRiPBroadPeak' > $FRiP_outfile
Expand Down Expand Up @@ -1671,12 +1689,14 @@ if [[ 0 == 1 ]]; then
if [[ ! -f $FRiP_outfile || $Overwrite == 1 ]]; then
# number of reads within MACS2 narrow peaks (q threshold = 0.05)
echo "# number of reads within MACS2 narrow peaks (q threshold = 0.05)"
macs2_nreads_narrowpeak=`samtools view -cL $QFilt1File $bowtie2_BAM_prefix'.rmdup.bam'`
#macs2_nreads_narrowpeak=`samtools view -cL $QFilt1File $bowtie2_BAM_prefix'.rmdup.bam'`
macs2_nreads_narrowpeak=`samtools view -L $QFilt1File $bowtie2_BAM_prefix'.rmdup.bam' | cut -f1 | sort -k1,1 | uniq | wc -l` # edited by Kyra, account for paired-end
FRiP_narrowpeak=`bc <<< "scale=3; ($macs2_nreads_narrowpeak * 1.0) / $uniq_mapped_read"`

# number of reads within MACS2 broad peaks (q threshold = 0.05)
echo "# number of reads within MACS2 broad peaks (q threshold = 0.05)"
macs2_nreads_broadpeak=`samtools view -cL $QFilt1FileBroad $bowtie2_BAM_prefix'.rmdup.bam'`
#macs2_nreads_broadpeak=`samtools view -cL $QFilt1FileBroad $bowtie2_BAM_prefix'.rmdup.bam'`
macs2_nreads_broadpeak=`samtools view -L $QFilt1FileBroad $bowtie2_BAM_prefix'.rmdup.bam' | cut -f1 | sort -k1,1 | uniq | wc -l` # edited by Kyra, account for paired-end
FRiP_broadpeak=`bc <<< "scale=3; ($macs2_nreads_broadpeak * 1.0) / $uniq_mapped_read"`

echo -e 'UniqMappedRead\tMappedReadNarrowpeak\tFRiPNarrowPeak\tMappedReadBroadpeak\tFRiPBroadPeak' > $FRiP_outfile
Expand Down Expand Up @@ -1929,12 +1949,14 @@ if [[ 0 == 1 ]]; then
if [[ ! -f $FRiP_outfile || $Overwrite == 1 ]]; then
# number of reads within MACS2 narrow peaks (q threshold = 0.05)
echo "# number of reads within MACS2 narrow peaks (q threshold = 0.05)"
macs2_nreads_narrowpeak=`samtools view -cL $QFilt1File $bowtie2_BAM_prefix'.rmdup.bam'`
#macs2_nreads_narrowpeak=`samtools view -cL $QFilt1File $bowtie2_BAM_prefix'.rmdup.bam'`
macs2_nreads_narrowpeak=`samtools view -L $QFilt1File $bowtie2_BAM_prefix'.rmdup.bam' | cut -f1 | sort -k1,1 | uniq | wc -l` # edited by Kyra, account for paired-end
FRiP_narrowpeak=`bc <<< "scale=3; ($macs2_nreads_narrowpeak * 1.0) / $uniq_mapped_read"`

# number of reads within MACS2 broad peaks (q threshold = 0.05)
echo "# number of reads within MACS2 broad peaks (q threshold = 0.05)"
macs2_nreads_broadpeak=`samtools view -cL $QFilt1FileBroad $bowtie2_BAM_prefix'.rmdup.bam'`
#macs2_nreads_broadpeak=`samtools view -cL $QFilt1FileBroad $bowtie2_BAM_prefix'.rmdup.bam'`
macs2_nreads_broadpeak=`samtools view -L $QFilt1FileBroad $bowtie2_BAM_prefix'.rmdup.bam' | cut -f1 | sort -k1,1 | uniq | wc -l` # edited by Kyra, account for paired-end
FRiP_broadpeak=`bc <<< "scale=3; ($macs2_nreads_broadpeak * 1.0) / $uniq_mapped_read"`

echo -e 'UniqMappedRead\tMappedReadNarrowpeak\tFRiPNarrowPeak\tMappedReadBroadpeak\tFRiPBroadPeak' > $FRiP_outfile
Expand Down