Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from https://grunwaldlab.github.io/demulticoder/reference/cut_trim.html below:

Main command to trim primers using 'Cutadapt' and core 'DADA2' functions — cut_trim • demulticoder

Main command to trim primers using 'Cutadapt' and core 'DADA2' functions

cut_trim(analysis_setup, cutadapt_path, overwrite_existing = FALSE)

analysis_setup

An object containing directory paths and data tables, produced by the prepare_reads function

cutadapt_path

Path to the 'Cutadapt' program.

overwrite_existing

Logical, indicating whether to remove or overwrite existing files and directories from previous runs. Default is FALSE.

Trimmed reads, primer counts, quality plots, and ASV matrix.

If samples are comprised of two different metabarcodes (like ITS1 and rps10), reads will also be demultiplexed prior to 'DADA2'-specific read trimming steps.

# \donttest{
# Remove remaining primers from raw reads, demultiplex pooled barcoded samples,
# and then trim reads based on specific 'DADA2' parameters
analysis_setup <- prepare_reads(
  data_directory = system.file("extdata", package = "demulticoder"),
  output_directory = tempdir(),
  overwrite_existing = TRUE
)
#> Existing files found in the output directory. Overwriting existing files.
#> Rows: 2 Columns: 25
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr  (3): primer_name, forward, reverse
#> dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo...
#> lgl  (4): already_trimmed, count_all_samples, multithread, verbose
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 2 Columns: 25
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr  (3): primer_name, forward, reverse
#> dbl (18): minCutadaptlength, maxN, maxEE_forward, maxEE_reverse, truncLen_fo...
#> lgl  (4): already_trimmed, count_all_samples, multithread, verbose
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 4 Columns: 3
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (3): sample_name, primer_name, organism
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Creating output directory: /tmp/RtmpAtZc28/demulticoder_run/prefiltered_sequences

cut_trim(
analysis_setup,
cutadapt_path="/usr/bin/cutadapt",
overwrite_existing = TRUE
)
#> Running cutadapt 3.5 for its sequence data

#> Running cutadapt 3.5 for rps10 sequence data

# }

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4