TnSeq data processing workflow

Michael Jahn, Johannes Asplund-Samuelsson

Description

The purpose of the following guide is to provide a simple, step-wise procedure for Tn-Seq data analysis. Tn-Seq (transposon sequencing) is the mapping of barcoded transposons to positions in a reference genome. This is the first of two major steps when analyzing barcoded transposon libraries. The second step is the extraction, PCR amplification, and sequencing of the already mapped barcodes from a transposon mutant library (see Price et al., Nature, 2018). The initial steps of processing next generation sequencing data was directly adapted from Morgan Price's Feba repository. The user is referred to the Feba repository or the original Tn-BarSeq publications for further information.

Prerequisites

• Linux environment with bash, perl and R installed
• the R packages tidyverse, stringi, rentrez, and RCurl (requires libcurl, install on ubuntu-flavored linux with sudo apt install libcurl4)
• a DNA alignment software, the default here is blat. It can be downloaded here and should be placed in feba/bin/. No compilation or setting of environmental flags is necessary. Check user permissions and make blat executable if it isn't (sudo chmod u+rwx blat).
• Perl scripts from Morgan Price's Feba repository, A. Arkin lab, Berkeley (see feba/bin/)
• Fastq sequencing data as obtained from Illumina runs (see data/fastq)
• Reference genome in .fasta format (stored in ref/, see description next section)
• Model file containing the structure of the read (see MODELS file in feba/primers/for more documentation)

Step 1: Retrieving data from Illumina basespace via command line (optional)

Data in form of *.fastq files can be manually downloaded from the basespace website on MacOS or Windows. For Linux systems, only the command line option is available via Illumina's BaseSpace Sequence Hub CLI (can be downloaded here). Files can be downloaded in .fastq.gz format for each biosample separately by executing the following line in a terminal and replacing <your-biosample-ID> with the number you will find in the URL of your browser. For example, log in to basespace, navigate to your run, then to biosamples, select a biosample and copy the ID you find in the URL: https://basespace.illumina.com/biosamples/568408389. Note that the files are subdivided per lane. More information can be found here.

bs download biosample -i <your-biosample-ID> -o ./your/target/directory/

Step 2: Select reference genome

The pipeline will automatically retrieve the correct genome sequence from NCBI. THe user will only need to visit NCBI genome hub and query the organism of choice:

https://www.ncbi.nlm.nih.gov/data-hub/genome/

For example, searching for the term Cupriavidus necator H16 will yield several entries, of which the first one is the correct one. The Assembly tag is the required input for the pipeline. For example:

• ASM928v2 -- Cupriavidus necator H16
• ASM2200v1 -- Caulobacter crescentus NA1000
• ASM21856v1 -- Afipia (Oligotropha) carboxidovorans OM5
• ASM435386v1 -- Hydrogenophaga pseudoflava DSM 1084

After running Step 3, the downloaded reference files (<assembly>.gff, <assembly>.gbk, <assembly>.fna) will be stored in the ./ref/ subfolder.

Step 3: Automated pipeline for barcode mapping

The automated pipeline is a bash script (run_tnseq_mapping.sh) that will execute the two main functions for barcode mapping for all *.fastq.gz files in /data/fastq/. Result tables will be stored in /data/mapped/, and data/pool/ by default. One pool file is created for all input files. The steps of the pipeline follow the description of the Feba workflow from Morgan Price. To run the pipeline, clone the repository and make sure you are in the TnSeq-pipe directory:

git clone https://github.com/m-jahn/TnSeq-pipe
cd TnSeq-pipe

The script takes the following optional arguments:

• --ref, the assembly tag from Step 2, e.g. (ASM928v2)
• --model, the read layout, default model_pKMW7 (see /feba/primers/)
• --data, the directory with input fastq files (default: data/fastq/)
• --pattern, run a subset of fastq files with a regex pattern (default: .*)
• --output, the directory where results are saved (default: data/)
• --stepSize, matching parameter passed on to low level function (default: -11)
• --tileSize, matching parameter passed on to low level function (default: -11)

For example, the following line will run the pipeline with custom options to use only fastq.gz files from Cupriavidus necator H16:

source/run_tnseq_mapping.sh --pattern H16.* --ref ASM928v2

Step 4: Transposon frequency and distribution

The statistical analysis of transposon insertion frequency and distribution over the genome is performed with a customized R notebook without using the tools from Morgan Price lab. The R notebook can be found in docs/TnSeq-pipe.Rmd together with the rendered output document docs/TnSeq-pipe.nb.html. The rendered R notebook can also be viewed directly via github pages using this link. Note that the appropriate reference genome needs to be set at line 49 of the script. The script generates two types of output:

• The annotated table pool_genes.tsv in data/pool/ that can be used as input for the BarSeq pipeline.
• Output figures for quality controls, for example the following:

Reads per barcode

Barcode frequency mapped per chromosome location

Transposon insertion frequency per location within genes

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Alternative to step 3: low-level functions

MapTnSeq.pl

The low-level functions of the pipeline can also be run independently (i.e. for debugging). First run the read mapping script MapTnSeq.pl. The following syntax and options are used with this script.

MapTnSeq.pl [ -debug ] [ -limit maxReads ] [ -minQuality $minQuality ]
            [-flanking $flanking]  [ -wobble $wobbleAllowed ]
            [ -minIdentity $minIdentity ] [ -minScore $minScore ] [ -delta $delta ]
            [ -tileSize $tileSize ] [ -stepSize $stepSize ]
            [-tmpdir $tmpdir ] [ -unmapped saveTo ] [ -trunc saveTo ]
            -genome fasta_file -model model_file -first fastq_file > output_file

• The output file is tab-delimited and contains, for each usable read, the read name, the barcode, which scaffold the insertion lies in, the position of the insertion, the strand that the read matched, a boolean flag for if this mapping location is unique or not, the beginning and end of the hit to the genome in the read after trimming the transposon sequence, the bit score, and the % identity.

• minQuality specifies the minimum quality score for each character in the barcode. flanking specifies the minimum number of nucleotides on each side that must match exactly.

• tileSize and stepSize are parameters for BLAT. If the portion of the read after the junction is short, try a lower stepSize. Also see BLAT's documentation.

• Use -unmapped or -trunc to save the portion of the reads past the junction. Only reads with barcodes and junctions are saved. -unmapped writes only the unmapped reads, in fasta format, with the barcode and the read name as the definition line. -trunc writes the remaining part of all of the reads with junctions, in fastq format, and it appends :barcode to the end of the read name (but before the space).

Example

In a terminal, run the following command with customized file paths. The example works with the data in this repository.

perl feba/bin/MapTnSeq.pl \
  -stepSize 7 -tileSize 7 \
  -genome ref/GCF_000009285.1_ASM928v2_genomic.fna \
  -model feba/primers/model_pKMW7 \
  -first data/fastq/H16_S2_L001_R1_001.fastq.gz \
  -unmapped data/mapped/H16_S2_L001_R1_001_unmapped.txt \
  -trunc data/mapped/H16_S2_L001_R1_001_truncated.txt \
  > data/mapped/H16_S2_L001_R1_001.tsv

DesignRandomPool.pl

From the Feba repository: DesignRandomPool.pl uses the output of MapTnSeq.pl to identify barcodes that consistently map to a unique location in the genome. These are the useful barcodes. Ideally, a mutant library has even insertions across the genome; has insertions in most of the protein-coding genes (except the essential ones); has a similar number of reads for insertions in most genes (i.e., no crazy positive selection for loss of a few genes); has insertions on both strands of genes (insertions on only one strand may indicate that the resistance marker's promoter is too weak); has tens of thousands or hundreds of thousands of useful barcodes; and the useful barcodes account for most of the reads.

The syntax for DesignRandomPool.pl is:

DesignRandomPool.pl -pool pool_file -genes genes_table [ -minN $minN ]
          [ -minFrac $minFrac ] [ -minRatio $minRatio ] [ -maxQBeg $maxQBeg ]
          MapTnSeq_file1 ... MapTnSeq_fileN

The script identifies the reliably mapped barcodes and writes a pool file as output. The MapTnSeq files must be tab-delimited with fields read, barcode, scaffold, pos, strand, uniq, qBeg, qEnd, score, identity where qBeg and qEnd are the positions in the read, after the transposon sequence is removed, that match the genome. Gzipped (*.gz) input files are also supported.

The genes table must include the fields scaffoldId, begin, end, strand, desc and it should either include only protein-coding genes or it should include the field 'type' with type=1 for protein-coding genes.

Example

Run the the following function in a terminal. Output is a tab-separated table with one unique transposn/barcode per row, its frequency and other data. All mapping tables matching the input pattern will be used to create the pool file (e.g data/mapped/*.tsv matches all tsv files).

perl feba/bin/DesignRandomPool.pl -minN 1 \
  -pool data/pool/H16_barcode_pool.tsv \
  -genes ref/GCF_000009285.1_ASM928v2_genomic_trimmed.tsv \
  data/mapped/H16_S2_L001_R1_001.tsv