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mourisl / Rcorrector

Error correction for Illumina RNA-seq reads
GNU General Public License v3.0
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write corrected reads to stdout #3

Closed macmanes closed 6 years ago

macmanes commented 9 years ago

Li: another enhancement

accept reads on stdin, write them to stdout.. 

seqtk mergepe $HOME/reads/kidney.1.fq.gz $HOME/reads/kidney.2.fq.gz \
  | skewer -l 25 -m pe --mean-quality $trim --end-quality $trim -t 8 -x $HOME/TruSeq3-PE.fa - -1 \
  | perl $HOME/Rcorrector/run_rcorrector.pl -t 8 -k 25 -i /dev/stdin -od /dev/stdout \
  | normalize-by-median.py --max-memory-usage 6e9 -C 30 -o - - \
  | jellyfish count -m 25 -s 700M -t 8 -C -o /dev/stdout /dev/stdin \
  | jellyfish histo /dev/stdin -o trimmed.yes.normalize.histo
mourisl commented 9 years ago

You can use "-stdout" to let Rcorrector output the result to stdout.