~ Run instructions

Now you should have collected the following :

Capturesite RE fragment coordinate file (CCseqBasicFragmentFile from CapSequm output)

List of genomic regions homologous to your capture RE fragments
( Optional ) - Can also be generated on-the-fly in the CCseqBasic run

List your input FASTQ files
(as --R1 and --R2 parameters, or as PIPE_fastqPaths.txt parameter file)

The below will cover the following :

Run the pipeline

Test dataset
Vignette for test run with test dataset
Browseable output files for the test dataset

(4) Run the pipeline

The help command of the pipe is a good place to start :

CCseqBasic5.sh  --help
CCseqBasic5.sh -h

Example run command

CCseqBasic5.sh \
    -c /t1-data/user/telenius/capturesiteREfragments.txt \
    -s C57captureTest \
    --pf /public/telenius/CAPTUREC_DATA/C57captureTest_run4 \
    --genome mm9 \
    --chunkmb 1012 \

and Fastq file locations in same command

    --R1 /t1-data/user/telenius/R1_001.fastq \
    --R2 /t1-data/user/telenius/R2_001.fastq \

or as a separate file in

PIPE_fastqPaths.txt

as descibed in : Input your FASTQ files and the fastq file type (if needed)

    --gz \

( and - optional but recommended

    --BLATforREUSEfolderPath /full/path/to/previous/run/F4_blatPloidyFiltering/REUSE_blat folder

: see page Generating homology regions lists )

The run should be started in an EMPTY FOLDER containing only

run.sh (the run script - if the above command is saved in a file)
PIPE_fastqPaths.txt

( See CCseqBasic5.sh --help , to see all possible run parameters ! )

Example run script

Example run.sh file available here : examplerun.sh

Test data set (no run instructions)

Test data set available here : exampledata

Full walk through (and test data set)

Walk through 'vignette' using the data set of original CaptureC method publication : walkthrough