# HG changeset patch # User jjohnson # Date 1331664286 14400 # Node ID 217aedbdd0d0b7c14102baf943be5880fe2b8a22 Uploaded diff -r 000000000000 -r 217aedbdd0d0 fastq-mcf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq-mcf.xml Tue Mar 13 14:44:46 2012 -0400 @@ -0,0 +1,204 @@ + + sequence quality filtering and clipping + + fastq-mcf + + fastq-mcf -V + fastq-mcf + #if $trimming.choice == 'disable': + -0 + #elif $trimming.choice == 'user_set': + #if len($trimming.scale.__str__) > 0 + -s $trimming.scale + #end if + #if len($trimming.minpct.__str__) > 0 + -t $trimming.minpct + #end if + #if len($trimming.nmin.__str__) > 0 + -m $trimming.nmin + #end if + #if len($trimming.pctdiff.__str__) > 0 + -p $trimming.pctdiff + #end if + #if len($trimming.nmax.__str__) > 0 + -L $trimming.nmax + #end if + #if len($trimming.nkeep.__str__) > 0 + -l $trimming.nkeep + #end if + #if len($trimming.skewpct.__str__) > 0 + -k $trimming.skewpct + #end if + #if len($trimming.qthr.__str__) > 0 + -q $trimming.qthr + #end if + #if len($trimming.qwin.__str__) > 0 + -w $trimming.qwin + #end if + #if len($trimming.pctns.__str__) > 0 + -x $trimming.pctns + #end if + #if len($trimming.sampcnt.__str__) > 0 + -s $trimming.sampcnt + #end if + $trimming.ilv3 + $trimming.rmns + #end if + #if $noclip == True : + $noclip + #else : + -o $reads_out + #if $mates.__str__ != 'None' : + -o $mates_out + #end if + #end if + $adpaters + $reads + #if $mates.__str__ != 'None' : + $mates + #end if + > $log + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + noclip == False + + + (noclip == False and mates != None) + + + + + +**What it does** + +fastq-mcf_ attempts to: + + Detect and remove sequencing adapters and primers + Detect limited skewing at the ends of reads and clip + Detect poor quality at the ends of reads and clip + Detect N's, and remove from ends + Remove reads with CASAVA 'Y' flag (purity filtering) + Discard sequences that are too short after all of the above + Keep multiple mate-reads in sync while doing all of the above + +.. _fastq-mcf: http://code.google.com/p/ea-utils/wiki/FastqMcf +----- + +**Input** + +Fasta file of adapter sequences, for example:: + + > Genomic_DNA_oligonucleotide_sequences_Adapters_F + GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG + > Genomic_DNA_oligonucleotide_sequences_Adapters_R + ACACTCTTTCCCTACACGACGCTCTTCCGATCT + > Genomic_DNA_Sequencing_Primer + ACACTCTTTCCCTACACGACGCTCTTCCGATCT + + + +Reads or Left-hand mates, for example:: + + @1539:931/1 + ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG + +1539:931/1 + BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB + +Right-hand mates, for example:: + + @1539:931/2 + CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT + +1539:931/2 + WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB + +----- + +**Output** + +A log file + +A trimmed fastq of the reads + +A trimmed fastq of the mates + + + + +