mfcovington/SHOREmap.log.mdown

## SHOREmap.log.mdown

      
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              SHOREmap.log.mdown
            
          
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SHORE
SHOREmap
SHORE example

#TEMPLATES
Extracting consensus sequences:
samtools mpileup -u        \
  -f _ref_.fa              \
  _aln_.bam                \
  | bcftools view -cg -    \
  | vcfutils.pl vcf2fq     \
  > _consensus_.fq

cat _consensus_.fq    \
  | perl -e 'use feature 'say';$i=0;while(<>){chomp;if(/^\@/../^\+/){if(/^\@/){$id=$_;$id =~ s/^\@/>/;say $id;$i=0;}elsif(/^\+/){print "\n";}else{print;$i++;}}else{<>for(1..$i-1);}}'   \
  > _consensus_.fa

SHORE import:
shore import                   \
  -v Fastq                     \
  -e Shore                     \
  -a genomic                   \
  -Q sanger                    \
  --disable-illumina-filter    \
  -o _output_dir_.shore        \
  -x _A_pe1_.fq,_B_pe1_.fq     \
  -y _A_pe2_.fq,_B_pe2_.fq

SHORE preprocess:
shore preprocess           \
  --bwa                    \
  -no-genomemapper         \
  -f _consensus_.fa        \
  -i _output_dir_.index    \

SHORE mapflowcell:
shore mapflowcell                 \
  -f _input_dir_.format           \
  -i _input_dir_.index/*.shore    \
  -v bwa                          \
  -n 4                            \
  -g 3                            \
  --cores=4                       \
  --PE                            \
  --rplot

SHORE consensus:
shore consensus                   \
  -n _ID_                         \
  -f _input_dir_.index/*.shore    \
  -i _input_dir_.shore            \
  -o _output_dir_.consensus       \
  -r