# 3'-end RNA-seq - 2016-08-24
# rna=t trimfragadapter=t qtrim=r trimq=6 maxns=1 maq=10 minlen=25 mlf=0.33 phix=t filterk=25 removehuman=t remove
#dog=t removecat=t removemouse=t khist=t removemicrobes=t

RQC Read Filtering Methods

Sequence data for library <library_name> was generated at the DOE Joint Genome Institute (JGI) using Illumina technology [1].  An Illumina <library_type> was constructed and
sequenced <sequencing_run_mode> using the Illumina <sequencer_name> platform which generated <raw_read_count> reads totaling <raw_base_count> bp.  BBDuk (version <bbtools_version>) [2]
was used to remove <contams_list> [3],  trim reads that contained RNA specific sequencing artifacts and right quality trim reads where quality drops below 6. Reads containing
1 or more 'N' bases, with average quality score across the read less than 10, having minimum length <= 49bp or 33% of the full read length, containing known Illumina artifacts
and reads mapping to PhiX, human, cat, dog and mouse at 93% identity were discarded [4].  Reads mapping to common contaminants were discarded [5].  The final filtered fastq
contained <filtered_read_count> reads totalling <filtered_base_count> bp. 

1. SOP 1070
2. B. Bushnell: BBTools software package, http:\\bbtools.jgi.doe.gov
3. bbduk parameters:
<rqc_filter_command>
4. All removed reads are placed in file:
<filter_chaff_fastq_file>
5. List of contaminants screened against:
Ralstonia solanacearum strain KACC 10722, Staphylococcus aureus strain V605, Escherichia coli str. K-12 substr. MG1655, Xanthomonas campestris pv. campestris str. ATCC 33913,
Ralstonia solanacearum GMI1000, Pseudomonas fluorescens SBW25, Bacillus halodurans C-125, Staphylococcus epidermidis RP62A, Pseudomonas fluorescens Pf0-1, Acidovorax sp. JS42,
Delftia acidovorans SPH-1, Stenotrophomonas maltophilia R551-3, Azoarcus sp. BH72, Stenotrophomonas maltophilia K279a, strain K279a, Comamonas testosteroni CNB-2,
Herbaspirillum seropedicae SmR1, Delftia sp. Cs1-4, Pseudomonas fluorescens F113, Rhizobium sp. AP16, Acidovorax sp. KKS102, Sphingomonas sp. MM-1, Curvibacter lanceolatus ATCC 14669,
Acinetobacter calcoaceticus ANC 3811, Burkholderia cepacia ATCC 25416, Rhizobium sp. LPU83, Pseudomonas sp. WCS374, Klebsiella oxytoca KONIH1, Cupriavidus basilensis strain 4G11,
Acidovorax temperans strain KY4, Cupriavidus gilardii CR3, Acinetobacter johnsonii XBB1, Acinetobacter baumannii strain XH857, Klebsiella pneumoniae subsp. pneumoniae HS11286,
Shigella dysenteriae Sd197, Shigella flexneri 2a str. 301
