Changes between Version 6 and Version 7 of SOPs/qc_shortReads
- Timestamp:
- 11/19/13 10:16:23 (11 years ago)
Legend:
- Unmodified
- Added
- Removed
- Modified
-
SOPs/qc_shortReads
v6 v7 91 91 # Sample commands: 92 92 # quality_stats: Sample Solexa reads file: s_1_1_sequence.txt or s_1_1_sequence.txt.gz 93 fastx_quality_stats -i s_1_1_sequence.txt -o s_1_1_sequence.stats 94 gunzip -c s_1_1_sequence.txt.gz | fastx_quality_stats -o s_1_1_sequence.stats 93 fastx_quality_stats -i s_1_1_sequence.txt -o s_1_1_sequence.stats # fastq input 94 gunzip -c s_1_1_sequence.txt.gz | fastx_quality_stats -o s_1_1_sequence.stats # fastq.gz input 95 95 # a figure for Nucleotide Distribution: 96 96 fastx_nucleotide_distribution_graph.sh -i s_1_1_sequence.stats -o s_1_1_sequence.stats.nuc.png -t "s_1_1_sequence.stats Nucleotide Distribution" … … 109 109 110 110 {{{ 111 fastq_quality_filter -v -q 20 -p 75 -i myFile.fastq -o myFile.fastq.fastx_trim 112 gunzip -c myFile.fastq | fastq_quality_filter -v -q 20 -p 75 - o myFile.fastq.fastx_trim111 fastq_quality_filter -v -q 20 -p 75 -i myFile.fastq -o myFile.fastq.fastx_trim # fastq input and output 112 gunzip -c myFile.fastq | fastq_quality_filter -v -q 20 -p 75 -z -o myFile.fastq.fastx_trim.gz # fastq.gz input and output 113 113 114 114 [-h] = This helpful help screen. … … 132 132 133 133 {{{ 134 bsub "fastq_quality_trimmer -v -t 20 -l 25 -i input.fastq -o output.fastq" 135 bsub "gunzip -c input.fastq.gz | fastq_quality_trimmer -v -t 20 -l 25 -z -o output.fastq.gz" 134 bsub "fastq_quality_trimmer -v -t 20 -l 25 -i input.fastq -o output.fastq" # fastq input and output 135 bsub "gunzip -c input.fastq.gz | fastq_quality_trimmer -v -t 20 -l 25 -z -o output.fastq.gz" # fastq.gz input and output 136 136 137 137 [-t N] = Quality threshold - nucleotides with lower … … 164 164 165 165 {{{ 166 bsub "fastx_clipper -a CTGTAGGCACCATCAAT -i s2_sequence.txt -v -l 22 -o s2_sequence_noLinker.txt" 167 bsub "gunzip -c s2_sequence.txt | fastx_clipper -a CTGTAGGCACCATCAAT -v -l 22 -z -o s2_sequence_noLinker.txt.gz" 166 bsub "fastx_clipper -a CTGTAGGCACCATCAAT -i s2_sequence.txt -v -l 22 -o s2_sequence_noLinker.txt" # fastq input and output 167 bsub "gunzip -c s2_sequence.txt | fastx_clipper -a CTGTAGGCACCATCAAT -v -l 22 -z -o s2_sequence_noLinker.txt.gz" # fastq.gz input and output 168 168 169 169 … … 191 191 192 192 {{{ 193 bsub "fastx_trimmer -f 1 -l 22 -i s7_sequence_clipped.txt -o s7_sequence_clipped_trimmed.txt" 194 bsub "gunzip -c s7_sequence_clipped.txt | fastx_trimmer -f 1 -l 22 -z -o s7_sequence_clipped_trimmed.txt.gz" 193 bsub "fastx_trimmer -f 1 -l 22 -i s7_sequence_clipped.txt -o s7_sequence_clipped_trimmed.txt" # fastq input and output 194 bsub "gunzip -c s7_sequence_clipped.txt | fastx_trimmer -f 1 -l 22 -z -o s7_sequence_clipped_trimmed.txt.gz" # fastq.gz input and output 195 195 196 196 [-i INFILE] = FASTA/Q input file. default is STDIN.
