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runBlast.sh
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runBlast.sh
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#!/usr/bin/sh
# Clint Valentine
# 10/13/2016
blastn \
-query ./trinity_out_dir/Trinity.fasta \
-evalue 1e-20 \
-db /blastDB/S_pombe_refTrans \
-dust no \
-task megablast \
-num_threads 2 \
-out ./Trinity_vs_S_pombe_refTrans.blastn \
-max_target_seqs 1 \
-outfmt 6
# USAGE
# blastn [-h] [-help] [-import_search_strategy filename]
# [-export_search_strategy filename] [-task task_name] [-db database_name]
# [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
# [-negative_gilist filename] [-entrez_query entrez_query]
# [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
# [-subject subject_input_file] [-subject_loc range] [-query input_file]
# [-out output_file] [-evalue evalue] [-word_size int_value]
# [-gapopen open_penalty] [-gapextend extend_penalty]
# [-perc_identity float_value] [-qcov_hsp_perc float_value]
# [-xdrop_ungap float_value] [-xdrop_gap float_value]
# [-xdrop_gap_final float_value] [-searchsp int_value] [-max_hsps int_value]
# [-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy]
# [-min_raw_gapped_score int_value] [-template_type type]
# [-template_length int_value] [-dust DUST_options]
# [-filtering_db filtering_database]
# [-window_masker_taxid window_masker_taxid]
# [-window_masker_db window_masker_db] [-soft_masking soft_masking]
# [-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
# [-best_hit_score_edge float_value] [-window_size int_value]
# [-off_diagonal_range int_value] [-use_index boolean] [-index_name string]
# [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]
# [-outfmt format] [-show_gis] [-num_descriptions int_value]
# [-num_alignments int_value] [-line_length line_length] [-html]
# [-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
# [-version]
# DESCRIPTION
# Nucleotide-Nucleotide BLAST 2.2.30+
# Use '-help' to print detailed descriptions of command line arguments