Package: scram
SCRAM-------------------SCRAM is lightweight Python package for aligning small RNA reads to oneor more reference sequences and producing publication-quality images.Developed by Stephen Fletcher @ the laboratory of Prof. Bernie Carroll,University of Queensland--------------*Installation:*Scram is written in Python 2.7. Install scram and its dependencies with``pip``:``pip install scram``Or download and extract the tarball, then run:``python setup.py install``--------------*Input File Format:*Reference File : DNA nucleotides only (AGCT) - FASTA formatSequence File : Collapsed reads - DNA nucleotides only (AGCT) - FASTAformatPost-processing of FASTQ reads to collapsed FASTA format can be carriedout using the `FASTX-Toolkit from the HannonLab <http://hannonlab.cshl.edu/fastx_toolkit/>`__. Collapsed reads areunique, and contain the read count in the header.An example of the required read file format:``head seq1.fa``::>1-607041TCGGACCAGGCATCATTCCCC>2-202886TCGGACCAGGCTTCATACCCC>3-71446TCCCAAATATAGACAAAGCA--------------*Usage:*``scram analysis_type reference_file [-h] [-s1 SEQ_FILE_1] [-s2 SEQ_FILE_2] [-s3 SEQ_FILE_3] [-s4 SEQ_FILE_4] [-nt SRNA_LEN] [-f FILE_NAME] [-seq_list SEQ_LIST] [-min_read MIN_READ_SIZE] [-max_read MAX_READ_SIZE] [-min_count MIN_READ_COUNT] [-win SMOOTH_WIN_SIZE] [-ylim YLIM] [-no_display] [-split] [-pub] [-V]``Analysis types-  **den** : align reads of a single sRNA class (eg. 21 nt) from asingle sequence file to a single reference sequence (-s1 and -ntrequired)-  **mnt3dm** : align 21, 22 and 24 nt reads from a single sequence fileto a single reference sequence (-s1 required)-  **CDP** : count aligned reads of a single sRNA class (eg. 21 nt) tomultiple reference sequences. Counts for two sequence files areplotted as (x,y) coordinates for each reference (-s1, -s2 and -ntrequired)Flags-  **-h** : Help message-  **-s1** : Sequence file 1-  **-s2** : Sequence file 2-  **-s3** : Sequence file 3-  **-s4** : Sequence file 4-  **-nt** : sRNA length to analyse-  **-f** : Figure output file name (if not auto-generated)-  **-p** : Number of cores (processors) to use (default=4)-  **-seq\_list** : Text (.txt) file with full path of sequence file oneach line (single replicate) or two tab-delimited sequence file pathsper line (two replicates)-  **-min\_read** : Minimum length of sRNA reads used for normalisation(default=18)-  **-max\_read** : Maximum length of sRNA reads used for normalisation(default=32)-  **-min\_count** : Minimum read count for an sRNA to be aligned andused for normalisation (default=1)-  **-win** : Window size for smoothing of den plots (default=50)-  **-ylim** : +/- y-axis limit on plots-  **-no\_display** : Do not display plot on screen-  **-no\_csv** : Do not generate .csv alignment file-  **-split** : Split CDP read alignment counts based on no. ofalignments-  **-pub** : Remove all labels from density maps for publication-  **-V** : Show program's version number and exit--------------den example:``scram den ./ref.fa -s1 seq1.fa -nt 24 -win 30 -f fig1.pdf``mnt3dm Example:``scram mnt3dm ./ref.fa -s1 seq1.fa -win 20 -ylim 110 -f fig2.pdf``CDP Example:``scram CDP ./cDNAs.fa -s1 seq1.fa -s2 seq2.fa -nt 21 -f fig3.pdf -split``--------------(c) 2016 - Stephen Fletcher. MIT License