Concatenate bbmerge output

Question

[ARich]

Dear Biostar users,

I am using bbmerge to create interleaved file using my paired end data.

$TOOLS_FOLDER/bbmap/bbmerge.sh \
    threads=4 \
    in1=${s} \
    in2=${s%1*}2.final.clean.fq \
    out=${s%1*}merged.final.clean.fq \
    outu1=${s%1*}1.unmerged.final.clean.fq \
    outu2=${s%1*}2.unmerged.final.clean.fq \
    mininsert=60 \

My question is can I concatenate the merged output which is (${s%1*}merged.final.clean.fq)` with my unpaired read output from bbwrap command ? Shown below:

$TOOLS_FOLDER/bbmap/bbwrap.sh \
    threads=16 \
    trimq=20 \
    minlength=60 \
    in=${s},${s%1*}unpaired.trimmoclean.sickleclean.bbdukclean.fq \
    in2=${s%1*}2.trimmoclean.sickleclean.bbdukclean.fq,NULL \
    outu1=${s%1*}1.final.clean.fq \
    outu2=${s%1*}2.final.clean.fq \
    outu=${s%1*}u.clean.fq \
    path=${REFERENCE_FOLDER}/mouse/

Thank you

Looking forward for reply!

Answer 1

[GenoMax]

bbwrap.sh is a wrapper program meant to be used for the following:

Wrapper for BBMap to allow multiple input and output files for the same reference.

This potentially allows you to align data where a R1/R2 file may be missing for a sample.

You can simply cat your unpaired read output at end of paired data (not sure why you would want to do that) if the only thing you want to do is to create a single file.