This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Concatenate bbmerge output

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!

next-gen
• 1,249 views • link
updated by Ram Ram • written by ARich ARich

1 answer

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.

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this