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mourisl / Rcorrector

Error correction for Illumina RNA-seq reads
GNU General Public License v3.0
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accept streaming interleaved reads #2

Open macmanes opened 9 years ago

macmanes commented 9 years ago

Li:

Enhancement: Accept interleaved reads with -i or --interleaved.

I'd like to do this: 

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 --interleaved -
mourisl commented 9 years ago

You can use "-i" to specify interleaved reads now.

Since Rcorrector scans the input several times, it is difficult to put it into pipeline in that fashion.