dokcer-asap2kite

A script to reformat FASTQ files from ASAP-seq for downstream processing.

Note that it was originally designed for kite (kallisto | bustools), but can be used for something else as well.

How to Run

docker run -it --rm \
    -v $(pwd)/test:/data \
    -w /data \
    asap2kite:0.0.1 \
    --fastqs /tmp/asap_to_kite-0.0.1/test/data1/ \
    --sample test1 \
    --id asapseq-test \
    --cores 2

Build Container Image

./build.sh

Push to Docker Registry

Either you can use the docker push command or run push.sh (requires SCING):

./push.sh

Structure

TotalSeq-A

Illumina demultiplexed:

• R1: UMI / UBI (10 nts) at position 0
• R2: CB (16 nts)
• R3: HTO (15 nts)
• I: Illumina indexing

After reformatted:

• R1: CB (16nts) + UMI (10 nts)
• R2: HTO (15 nts) at position 0

Conversion code: https://github.com/hisplan/asap_to_kite/blob/master/asap_to_kite_v2.py#L122

Notes

• R2 from sequencing must have exactly 16 nts. It appears that >16 could cause issues during the reformatting.