QTrim

[…] depth of 800x. sequence quality was examined using fastqc (rrid:scr_014583, http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) and sequence reads were quality trimmed (parameters: minlen = 50 qtrim = rl trimq = 15 ktrim = r k = 21 mink = 8 ref=$adapters hdist = 2 hdist2 = 1 tbo = t tpe = t) and cleared of human (parameters: minid = 0.95 maxindel = 3 bwr = 0.16 bw = 12 quickmatch fast […]

[…] rl trimq = 15 ktrim = r k = 21 mink = 8 ref=$adapters hdist = 2 hdist2 = 1 tbo = t tpe = t) and cleared of human (parameters: minid = 0.95 maxindel = 3 bwr = 0.16 bw = 12 quickmatch fast minhits = 2 qtrim = lr trimq = 10) and phix (parameters: k = 31 hdist = 1) sequences against the whole respective genomes using bbmap v35 (http://sourceforge.net/projects/bbmap/)., for pacbio sequencing, bsv […]

[…] inc., san diego, ca, usa). samples were sequenced twice in separated lanes. paired-end (2 × 100 bp) and raw reads were pre-processed for quality using fastqc 0.11.21 and adapter trimming with qtrim v0.942. the resulting pre-processed reads were aligned to the reference transcriptome of vitis vinifera (v1 grapevine annotation)3 using the bowtie2 aligner v2.2.3 (langmead and salzberg, 2012) […]