pints_visualizer

Reference Code backup Executable files

Extract Transcription Start Sites (TSSs) from a bam file and save extracted signal into strand specific bigwig files

Category

Sam/Bam Manipulation

Usage

pints_visualizer -b sample.bam -o sample -e ExperimentType

Manual

Options

  • -b BAM, --bam BAM: the input file
  • -e BAM_PARSER, --exp-type BAM_PARSER: Type of experiment, acceptable values are: CoPRO/GROcap/GROseq/PROcap/PROseq, or if you know the position of RNA ends which you're interested on the reads, you can specify R_5 (the 5' end of the read, for single-end libraries), R_3 (the 3' end of the read, for single-end libraries), R1_5 (the 5' end of the read 1, for paired-end libraries), R1_3 (the 3' end of the read 1, for paired-end libraries), R2_5 (the 5' end of the read 2, for paired-end libraries) or R2_3 (the 3' end of the read 2, for paired-end libraries)
  • -r, --reverse-complement: Set this switch if reads in this library represent the reverse complement of nascent RNAs, like PROseq
  • -c, --rpm: Set this switch if you want to use RPM to normalize the outputs
  • --mapq-threshold MAPQ_THRESHOLD: Minimum mapping quality
  • --chromosome-start-with CHROMOSOME_STARTSWITH: Only keep reads mapped to chromosomes with this prefix
  • -o OUTPUT_PREFIX, --output-prefix OUTPUT_PREFIX: The output BigWig files will have a prefix specified by this option
  • -f [FILTERS ...], --filters [FILTERS ...]: reads from chromosomes whose names contain any matches in filters will be ignored
  • -n NORM_FACT, --norm-fact NORM_FACT: Final signals in the output bigwig files will be the raw coverage times the normalization factor. By default 1
  • -s, --cache: Set this switch if you want to reuse the intermediate .npy files.
  • -h, --help: show this help message and exit
  • -v, --version: show program's version number and exit

Example

The following command will generate two bigWig files called SampleA_pl.bw and SampleA_mn.bw for an aligned GRO-cap library (SampleA_Aligned.sortedByCoord.out.bam).

pints_visualizer -b SampleA_Aligned.sortedByCoord.out.bam \  # the input bam file
                 -e GROcap \  # reads are in the same direction as RNAs, and only report the 5′ end of reads in the output
                 --mapq-threshold 255 \  # only consider uniquely mapped reads
                 --chromosome-start-with chr \  # only reads mapped to contigs start with chr will be included
                 -o SampleA  # prefix for outputs

Protocols using this tool

PROcap preprocessing (with two replicates)

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