'''Almost all steps of a short-read analysis pipeline can use fastq.gz (gzipped) files, rather than fastq, to save storage space.  For example,'''

# Untar from solexa_public, gunzip, and gzip \\
tar -xOzf /lab/solexa_public/LAB/RUN/QualityScore/Foo.1.tar.gz | gzip -f > fastq/My_sample.1.fq.gz \\
tar -xOzf /lab/solexa_public/LAB/RUN/QualityScore/Foo.2.tar.gz | gzip -f > fastq/My_sample.2.fq.gz \\

# [Whitehead fastq files only] Untar from solexa_public, gunzip, remove WI GTC-specific header suffixes and gzip \\
tar -xOzf /lab/solexa_public/LAB/RUN/QualityScore/Foo.1.tar.gz | /nfs/BaRC_Public/BaRC_code/Perl/rm_WI_Illumina_suffix/rm_WI_Illumina_suffix.STDIN.pl | gzip -f > fastq/My_sample.1.fq.gz \\
tar -xOzf /lab/solexa_public/LAB/RUN/QualityScore/Foo.2.tar.gz | /nfs/BaRC_Public/BaRC_code/Perl/rm_WI_Illumina_suffix/rm_WI_Illumina_suffix.STDIN.pl | gzip -f > fastq/My_sample.2.fq.gz \\

# Run FastQC \\
fastqc fastq/My_sample.1.fq.gz \\
fastqc fastq/My_sample.2.fq.gz \\

# Trim adapters \\
gunzip -c fastq/My_sample.1.fq.gz | fastx_clipper -v -z -l 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG -o fastq/My_sample.noVec.1.fq.gz \\
gunzip -c fastq/My_sample.2.fq.gz | fastx_clipper -v -z -l 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG -o fastq/My_sample.noVec.2.fq.gz \\
fastqc fastq/My_sample.noVec.1.fq.gz \\
fastqc fastq/My_sample.noVec.2.fq.gz \\

# Drop reads of low quality \\
gunzip -c fastq/My_sample.noVec.1.fq.gz | fastq_quality_filter -v -q 20 -p 75 -z -o fastq/My_sample.noVec.qgt20.1.fq.gz \\
gunzip -c fastq/My_sample.noVec.2.fq.gz | fastq_quality_filter -v -q 20 -p 75 -z -o fastq/My_sample.noVec.qgt20.2.fq.gz \\

# Trim low-quality bases at end of reads \\
gunzip -c fastq/My_sample.noVec.qgt20.1.fq.gz | fastq_quality_trimmer -v -t 20 -l 30 -o fastq/My_sample.noVec.qgt20.t.1.fq \\
gunzip -c fastq/My_sample.noVec.qgt20.2.fq.gz | fastq_quality_trimmer -v -t 20 -l 30 -o fastq/My_sample.noVec.qgt20.t.2.fq \\

# After trimming, get reads that are still paired (and output as regular fastq for next (bowtie) step) \\
# We hope to modify cmpfastq.pl to accept gz files as input \\
/nfs/BaRC_Public/BaRC_code/Perl/cmpfastq/cmpfastq.pl fastq/My_sample.noVec.qgt20.t.1.fq fastq/My_sample.noVec.qgt20.t.2.fq

# Map paired reads with bowtie \\
# '''bowtie cannot use gzipped input files''' \\
bowtie -l 30 -n 1 -X 1000 --best -S /nfs/genomes/GENOME/bowtie/INDEX -1 fastq/My_sample.noVec.qgt20.t.1.fq-common.out -2 fastq/My_sample.noVec.qgt20.t.2.fq-common.out mapped_reads/My_sample.30.1.sam

# Sort and index mapped reads \\
/nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl mapped_reads/My_sample.30.1.sam \\
# Delete SAM file (since BAM file has all the same info) \\
rm -f mapped_reads/My_sample.30.1.sam \\

# Get summary counts \\
zcat fastq/My_sample.1.fq.gz | echo $((`wc -l`/4)) \\
zcat fastq/My_sample.noVec.1.fq.gz | echo $((`wc -l`/4)) \\
zcat fastq/My_sample.noVec.2.fq.gz | echo $((`wc -l`/4)) \\
zcat fastq/My_sample.noVec.qgt20.1.fq.gz | echo $((`wc -l`/4)) \\
zcat fastq/My_sample.noVec.qgt20.2.fq.gz | echo $((`wc -l`/4)) \\
more fastq/My_sample.noVec.qgt20.t.1.fq | echo $((`wc -l`/4)) \\
more fastq/My_sample.noVec.qgt20.t.2.fq | echo $((`wc -l`/4)) \\
zmore fastq/My_sample.noVec.qgt20.t.1.fq-common.out.gz | echo $((`wc -l`/4)) \\
samtools flagstat mapped_reads/My_sample.30.1.sorted.bam > mapped_reads/My_sample.30.1.flagstat.txt \\
grep ' mapped (' mapped_reads/My_sample.30.1.flagstat.txt