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Hello, I’m using rcorrector, but I have a problem with Bad quality threshold of ",", I am not sure whether it is correct. The version I I’m using is Rcorrector v1.0.4. My code and the messages as below:
_libs=CT2-1NOV R2=(ls -1 fastq/${libs[$i]}*_R2.fastq.gz |perl -p -e 's/\n/,/' |perl -p -e 's/,$//' ) perl ~/software/rcorrector/runrcorrector.pl -s ${R2[0]} -k 25 -od ./fastq/Rcorrected -t 72
ls -1 fastq/${libs[$i]}*_R2.fastq.gz |perl -p -e 's/\n/,/' |perl -p -e 's/,$//'
_Put the kmers into bloom filter ~/software/rcorrector/jellyfish/bin/jellyfish bc -m 25 -s 100000000 -C -t 72 -o tmp_2418d35a9613770b55070763b9d631.bc <(gzip -cd CT2-1NOV_R2.fastq.gz) Count the kmers in the bloom filter ~/software/rcorrector/jellyfish/bin/jellyfish count -m 25 -s 100000 -C -t 72 --bc tmp_2418d35a961377ea55070763b9d631.bc -o tmp_2418d35a9613770bea55070763b9d631.mer_counts <(gzip -cd CT2-1NOV_R2.fastq.gz) Dump the kmers ~/software/rcorrector/jellyfish/bin/jellyfish dump -L 2 tmp_2418d35a9613770bea55070763b9d631.mer_cous > tmp_2418d35a9613770bea55070763b9d631.jf_dump Error correction ~/software/rcorrector/rcorrector -k 25 -od ./fastq/Rcorrected -t 72 -r CT2-1NOV_R2.fastq.gz -c tmp_18d35a9613770bea55070763b9d631.jfdump Stored 260713828 kmers Weak kmer threshold rate: 0.134733 (estimated from 0.950/1 of the chosen kmers) Bad quality threshold is ',' Processed 163121995 reads Corrected 103221456 bases.
Additional information： _grep -c "@" CT2-1NOV_R2.fastq.gz 31371319 grep -c "@" CT2-1NOV_R2.cor.fq.gz 34040608 zcat CT2-1NOV_R2.cor.fq.gz | tail -n 20 @J00102:34:HVW3JBBXX:1:2228:30807:49247 2:N:0:NTACTCAG l:16105 m:28357 h:30170 cor TGAGGAATGTTGTGCAGAGTTTATATTTTTTAAAATAGTGTTCATAAAGAAATACCTATCATTCCTTTTTCCAAAGTAGTGGGAGAAATTATCTCATTGT +
@J00102:34:HVW3JBBXX:1:2228:30888:49247 2:N:0:NTACTCAG l:11974 m:16348 h:26600 cor GAGGCCCTCTGGCTTCTCATTTTCCATTCCTCTCGCCCAGCTAAGGGGTAGGGGTGAGGGGACTGGGGAGGGAGGGTTGCCCACTGCGGGCTGGGGCTTG +
@J00102:34:HVW3JBBXX:1:2228:31477:49247 2:N:0:NTACTCAG l:34 m:75 h:231 cor ATCTAAGACAGCGGATGCGGTGGCTGGGATACCAATATTTGAACTCCTCATAAGATAAGCATTGTAATGCCCAGGGAGCAGGGTAGGCAGGTGGGTCTGA +
@J00102:34:HVW3JBBXX:1:2228:31619:49247 2:N:0:NTACTCAG l:37527 m:46054 h:112386 cor GTCATGCTCAAAGGCTGCGTCGTGGGGACCAAGAAGCGAGTGCTCACCCTTCGCAAGTCCTTGCTGGTACAGACCAAACGACGGGCCCTGGAGAAGATCG +
@J00102:34:HVW3JBBXX:1:2228:32065:49247 2:N:0:NTACTCAG l:3489 m:7152 h:8223 cor GTCCCATGTACATCATTAGGCAGAAGAACAACAAATATGTTCTTAAGCAGAGGTCATCTACCCTACTTCCCAGTGGAAACCAAACCCTCCAGCGGGTCCT +
Thanks for your help!
Hello, I’m using rcorrector, but I have a problem with Bad quality threshold of ",", I am not sure whether it is correct. The version I I’m using is Rcorrector v1.0.4. My code and the messages as below:
_libs=CT2-1NOV R2=(
ls -1 fastq/${libs[$i]}*_R2.fastq.gz |perl -p -e 's/\n/,/' |perl -p -e 's/,$//') perl ~/software/rcorrector/runrcorrector.pl -s ${R2[0]} -k 25 -od ./fastq/Rcorrected -t 72_Put the kmers into bloom filter ~/software/rcorrector/jellyfish/bin/jellyfish bc -m 25 -s 100000000 -C -t 72 -o tmp_2418d35a9613770b55070763b9d631.bc <(gzip -cd CT2-1NOV_R2.fastq.gz) Count the kmers in the bloom filter ~/software/rcorrector/jellyfish/bin/jellyfish count -m 25 -s 100000 -C -t 72 --bc tmp_2418d35a961377ea55070763b9d631.bc -o tmp_2418d35a9613770bea55070763b9d631.mer_counts <(gzip -cd CT2-1NOV_R2.fastq.gz) Dump the kmers ~/software/rcorrector/jellyfish/bin/jellyfish dump -L 2 tmp_2418d35a9613770bea55070763b9d631.mer_cous > tmp_2418d35a9613770bea55070763b9d631.jf_dump Error correction ~/software/rcorrector/rcorrector -k 25 -od ./fastq/Rcorrected -t 72 -r CT2-1NOV_R2.fastq.gz -c tmp_18d35a9613770bea55070763b9d631.jfdump Stored 260713828 kmers Weak kmer threshold rate: 0.134733 (estimated from 0.950/1 of the chosen kmers) Bad quality threshold is ',' Processed 163121995 reads Corrected 103221456 bases.
Additional information： _grep -c "@" CT2-1NOV_R2.fastq.gz 31371319 grep -c "@" CT2-1NOV_R2.cor.fq.gz 34040608 zcat CT2-1NOV_R2.cor.fq.gz | tail -n 20 @J00102:34:HVW3JBBXX:1:2228:30807:49247 2:N:0:NTACTCAG l:16105 m:28357 h:30170 cor TGAGGAATGTTGTGCAGAGTTTATATTTTTTAAAATAGTGTTCATAAAGAAATACCTATCATTCCTTTTTCCAAAGTAGTGGGAGAAATTATCTCATTGT +
A-<F7F<<<FAAJFJFAF<<FFJFJFJJJJ----<--<-AJ--7<A<A--7--7---A<7<FF<JJFJJ7---7<--7-7AF-7----<-AFA<-<--7
@J00102:34:HVW3JBBXX:1:2228:30888:49247 2:N:0:NTACTCAG l:11974 m:16348 h:26600 cor GAGGCCCTCTGGCTTCTCATTTTCCATTCCTCTCGCCCAGCTAAGGGGTAGGGGTGAGGGGACTGGGGAGGGAGGGTTGCCCACTGCGGGCTGGGGCTTG +
A<FFA7FAFFJAJFJF<JFJJJJFFJJFJJJJFJFJJFJJJFFJFJJ77AJJJFJ7JFFFAJJJFJJ-AFJ<FAJJJJJJJJJ<FJJJJJFJJJF777F
@J00102:34:HVW3JBBXX:1:2228:31477:49247 2:N:0:NTACTCAG l:34 m:75 h:231 cor ATCTAAGACAGCGGATGCGGTGGCTGGGATACCAATATTTGAACTCCTCATAAGATAAGCATTGTAATGCCCAGGGAGCAGGGTAGGCAGGTGGGTCTGA +
A<<F-7<FFA7<-FFFJ7-AAJJJJ-7---77FAF-AJ--<7<F7-F-7-<7A-<-777--F<A--77--7---7FJ--F--AA7F-<7-AA---7F--
@J00102:34:HVW3JBBXX:1:2228:31619:49247 2:N:0:NTACTCAG l:37527 m:46054 h:112386 cor GTCATGCTCAAAGGCTGCGTCGTGGGGACCAAGAAGCGAGTGCTCACCCTTCGCAAGTCCTTGCTGGTACAGACCAAACGACGGGCCCTGGAGAAGATCG +
--<-7--FJFJJ7------7--7--7A7-AF<J-AF-77AAA-7<F--7---77<7F7F-<F-<<7-A-<7<---7--7---7AAA7JJ<A77FJ7F--
@J00102:34:HVW3JBBXX:1:2228:32065:49247 2:N:0:NTACTCAG l:3489 m:7152 h:8223 cor GTCCCATGTACATCATTAGGCAGAAGAACAACAAATATGTTCTTAAGCAGAGGTCATCTACCCTACTTCCCAGTGGAAACCAAACCCTCCAGCGGGTCCT +
<<-<<<FJJFFFJ7FJ<AFFAFF7<-F7-AJ<-JFJJFAJF-FA<A<AFA<AAFAAJ7A7-7-A-FA--7-7<-J--<7-AFAJFAJJ<<A-7<<---7_
Thanks for your help!