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@@ -4,7 +4,7 @@
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%# BASICS
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%- \acs{DNA} STRUCTURE
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%- DATA TYPES
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-% - BAM/FASTQ
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+% - BAM/\ac{FASTQ}
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% - NON STANDARD
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%- COMPRESSION APPROACHES
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% - SAVING DIFFERENCES WITH GIVEN BASE \acs{DNA}
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@@ -40,7 +40,7 @@ Some common fileformats would be:
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\begin{itemize}
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% which is relevant?
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\item{FASTA}
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- \item{FASTQ}
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+ \item{\ac{FASTQ}}
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\item{twoBit}
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\item{SAM/BAM}
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\item{VCF}
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@@ -52,9 +52,9 @@ Since methods to store this kind of Data are still in development, there are man
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%rewrite:
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In order to not go beyond the scope, this paper will only focuse on compression tools which are using standard formats.
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-\section{FASTQ}
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+\section{\ac{FASTQ}}
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Is a text base format for storing sequenced data. It saves nucleotides as letters and in extend to that, the quality values are saved.
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-FASTQ files are split into multiples of four, each four lines contain the informations for one sequence. The exact structure of FASTQ format is as follows:
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+\ac{FASTQ} files are split into multiples of four, each four lines contain the informations for one sequence. The exact structure of \ac{FASTQ} format is as follows:
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\texttt{
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Line 1: Sequence identifier aka. Title, starting with an @ and an optional description.\\
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Line 2: The seuqence consisting of nucleoids, symbolized by A, T, G and C.\\
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@@ -65,9 +65,9 @@ The quality values have no fixed type, to name a few there is the sanger format,
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The quality value shows the estimated probability of error in the sequencing process.
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[...]
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-\section{SAM/BAM}
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+\section{Sequence Alignment Map}
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% src https://github.com/samtools/samtools
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-\ac{SAM} often seen in its compressed, binary representation \ac{BAM} with the fileextension \texttt{.bam}, is part of the SAMtools package, a uitlity tool for processing SAM/BAM and CRAM files. The SAM/BAM file is a text based format delimited by TABs. It uses 7-bit US-ASCII, to be precise Charset ANSI X3.4-1968 as defined in RFC1345. The structure is more complex than the one in FASTQ and described best, accompanied by an example:
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+\ac{SAM} often seen in its compressed, binary representation \ac{BAM} with the fileextension \texttt{.bam}, is part of the SAMtools package, a uitlity tool for processing SAM/BAM and CRAM files. The SAM/BAM file is a text based format delimited by TABs. It uses 7-bit US-ASCII, to be precise Charset ANSI X3.4-1968 as defined in RFC1345. The structure is more complex than the one in \ac{FASTQ} and described best, accompanied by an example:
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\begin{figure}[ht]
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\centering
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@@ -89,7 +89,7 @@ The regulare expression, shown above, filters touple of characters from a to z i
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%- allows viewing BAM data (localy and remote via ftp/http)
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%- file extention: <filename>.bam.bai
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-%- stores more data than FASTQ
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+%- stores more data than \ac{FASTQ}
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% src: https://support.illumina.com/help/BS_App_RNASeq_Alignment_OLH_1000000006112/Content/Source/Informatics/BAM-Format.htm
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%- allignment section includes
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@@ -102,6 +102,6 @@ The regulare expression, shown above, filters touple of characters from a to z i
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%- BAM index files nameschema: <filename>.bam.bai
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-\section{CRAM - Compressed Reference-oriented Ailgnment Map}
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+\section{Compressed Reference-oriented Ailgnment Map}
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\ac{CRAM} was developed as an alternative to the \ac{SAM} and \ac{BAM} Format. It specification is maintained by \ac{GA4GH}. It features both lossy and lossless compression mode. Since it is not relevant to this work, the lossy compression is ignored from here on. Even though it is part of \ac{GA4GH} suite, the file format can be used independently.\\
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The format saves data in containers which consist out of slices. Each slice is represented by a line in the file. Container and slices each store metadata in a header. Data is stored as blocks in slices, in a compressed form.
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