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Update Running Platypus Docker
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@cmargerum
cmargerum authored Sep 14, 2017
1 parent 8c878a1 commit dcb8a96
Showing 1 changed file with 6 additions and 4 deletions.
10 changes: 6 additions & 4 deletions Platypus/Running Platypus Docker
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Expand Up @@ -44,7 +44,7 @@ We need to prep your bam file for Opossum and Platypus, do so by entering:

samtools index $input
samtools view $input -b -o SAMPLE_PREOPOSSUM.bam chrZ:x-y
samtools calmd SAMPLE_PREOPOSSUM.bam /data/ref/$refgenome
samtools calmd –b SAMPLE_PREOPOSSUM.bam /data/ref/$refgenome > SAMPLE_PREOPOSSUM.calmd.bam

Note:
Replace SAMPLE_PREOPOSSUM.bam with the name you wish for the output and change chrZ:x-y with
Expand All @@ -57,11 +57,13 @@ Now your file is ready for Opossum. Platypus typically only works on DNA samples
through and adds the introns back into the samples, so Platypus doesn't get confused. Run Opossum on your
file with the following command:

python /root/Opossum/Opossum.py --SoftClipsExist=True --BamFile=SAMPLE_PREOPOSSUM.bam --OutFile=SAMPLE_POSTOPOSSUM.bam
python /root/Opossum/Opossum.py \
--SoftClipsExist=True \
--BamFile=SAMPLE_PREOPOSSUM.calmd.bam \
--OutFile=SAMPLE_POSTOPOSSUM.bam

Note:
Replace SAMPLE_PREOPOSSUM.bam and SAMPLE_POSTOPOSSUM.bam

Replace SAMPLE_PREOPOSSUM.bam, SAMPLE_POSTOPOSSUM.bam, and SAMPLE_POSTOPOSSUM.calmd.bam

7.
Platypus is now able to handle your file. Run it with the following command:
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