usage: patsy-align [-h] -1 fq1 -2 fq2 -f ref [-o outdir] [-s stats_pickle]
                   [-l gtail_sig] [-G gtag_min] [-N max_N] [-I min_fsize]
                   [-X max_fsize] [-p nr_threads] [-r report]

Align PAT-seq reads using Bowtie2 (1.1).

optional arguments:
  -h, --help       show this help message and exit
  -1 fq1           First FASTQ file.
  -2 fq2           Second FASTQ file.
  -f ref           Reference fasta.
  -o outdir        Output directory.
  -s stats_pickle  Stats pickle file.
  -l gtail_sig     Portion of read start/end used for G-tail classification
                   (14).
  -G gtag_min      Minimum G-tag length(3).
  -N max_N         Maximum number of Ns in the first -l bases (6).
  -I min_fsize     Minimum fragment size (0).
  -X max_fsize     Maximum fragment size (500).
  -p nr_threads    Number of threads to use (1).
  -r report        Report PDF.

usage: patsy-parse [-h] -g gtail_sam -n nvtr_sam -d dataset_id -f ref
                   [-l gtail_sig] [-G gtag_min] [-N max_N] [-e err_tol]
                   [-o out_pickle] [-i tr_list] [-q min_q] [-r report] [-t]

Parse classified and aligned PAT-seq read pairs (1.1).

optional arguments:
  -h, --help     show this help message and exit
  -g gtail_sam   SAM file containing G-tail alignments.
  -n nvtr_sam    SAM file containing NVTR alignments.
  -d dataset_id  Dataset identifier.
  -f ref         Reference fasta.
  -l gtail_sig   Portion of read start/end used for G-tail classification.
  -G gtag_min    Minimum G-tag length(3).
  -N max_N       Maximum number of Ns in the first -l bases (6).
  -e err_tol     Number of errors tolerated in the tail.
  -o out_pickle  Output pickle file.
  -i tr_list     List of transcripts considered.
  -q min_q       Mapping quality treshold (30).
  -r report      Report PDF.
  -t             Plot per-transcript coverage reports.

usage: patsy-test [-h] -a [a_pickles [a_pickles ...]] -na a_name -b
                  [b_pickles [b_pickles ...]] -nb b_name [-i lrt_list]
                  [-P lik_penalty] [-M min_size_U] [-s sig_level]
                  [-op out_pickle] [-ot out_trs] [-og out_glob]
                  [-otr out_runs_prefix] [-orr out_rep_prefix] [-r report]
                  [-t]

Test for differential polyadenylation in PAT-seq data (1.1).

optional arguments:
  -h, --help            show this help message and exit
  -a [a_pickles [a_pickles ...]]
                        Parsed read pickles - group A.
  -na a_name            Name of data group A.
  -b [b_pickles [b_pickles ...]]
                        Parsed read pickles - group B.
  -nb b_name            Name of data group B.
  -i lrt_list           Transcripts to be tested with anchors LRT.
  -P lik_penalty        Log-likelihood penalty for data points outside valid
                        range.
  -M min_size_U         Minimum sample size when performing Mann-Whitney U
                        test (30).
  -s sig_level          Significance level.
  -op out_pickle        Output pickle file.
  -ot out_trs           Output tabular file: transcript properties.
  -og out_glob          Output tabular file: global results.
  -otr out_runs_prefix  Output tabular file: tail runs prefix.
  -orr out_rep_prefix   Output tabular file: tail means per replicate.
  -r report             Report PDF.
  -t                    Plot reports for all transcripts.

usage: patsy-spike [-h] -n spike_sam -f ref [-w window] [-m max_errors_plot]
                   [-o out_pickle] [-q min_q] [-r report] [-l read_len]
                   [-pk pickle]

Estimate the number of sequencing errors in runs of bases (1.0).

optional arguments:
  -h, --help          show this help message and exit
  -n spike_sam        SAM file containing NVTR alignments.
  -f ref              Reference fasta with the spike-in sequences.
  -w window           Size of the flanking sequence around the run of As.
  -m max_errors_plot  Maximum number of errors for which to plot the length
                      distribution.
  -o out_pickle       Output pickle file.
  -q min_q            Mapping quality treshold (30).
  -r report           Report PDF.
  -l read_len         Read length.
  -pk pickle          Result pickle file.