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BinPro / CONCOCT

Clustering cONtigs with COverage and ComposiTion
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Example of concoct workflow #194

Closed johanneswerner closed 4 years ago

johanneswerner commented 6 years ago

I was following the workflow to run concoct on one of my samples but I faced problems when mapping the reads back to the contigs, more precisely here:

I installed concoct and picard via conda. 

export MRKDUP=/home/username/src/picard-tools-1.77/MarkDuplicates.jar
for f in $CONCOCT_TEST/reads/*_R1.fa; do
    mkdir -p map/$(basename $f);
    cd map/$(basename $f);
    bash $CONCOCT/scripts/map-bowtie2-markduplicates.sh -ct 1 -p '-f' $f $(echo $f | sed s/R1/R2/) pair $CONCOCT_EXAMPLE/contigs/velvet_71_c10K.fa asm bowtie2;
    cd ../..;
done

Picard is now available in version 2.18.7 and has no script MarkDuplicates.jar anymore.

Can you help me out here? Or is there another possibility to create the coverage and the linkage table and run concoct?

Thank you for your help. If you require any additional information, please ask.

johanneswerner commented 6 years ago

Just saw, that this is a duplicate of this comment in issue #180.

alneberg commented 4 years ago

The coverage table can now be created from a set of bam files and no specific script for mapping is longer recommended.