Analysis CAMDA

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Serghei Mangul edited this page Jul 13, 2017 · 3 revisions

Ameoba

while read line;do echo "bwa mem -a /u/home/s/serghei/project/eupathdb/eupathdbFasta_cat/ameoba_ConcatContigs.fa ~/collab/MetaSUB-Inter-City-Challenge/data/${line}.fastq | samtools view -bS - | samtools view -b -F 4 >${line}.bam">run_${line}.sh;done<../samples.txt

Map reads BWA

/u/home/s/serghei/scratch/metasub

while read line;do echo "bwa mem -a /u/project/zarlab/malser/MiCoP/fungi_ConcatContigs.fa ~/collab/MetaSUB-Inter-City-Challenge/data/${line}.fastq | samtools view -bS - | samtools view -b -F 4 >${line}.bam">run_${line}.sh;done<samples.txt

Cov plots

samtools view -h SRR1748536.bam >SRR1748536.sam
python /u/home/s/serghei/code/miCoP/CoveragePlot/ReadClassifier.py SRR1748536.sam 1 >SRR1748536_UNIQ.sam