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parameter.md

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Parameter Set in PipeOne-NM

Parameters that are not mentioned specifically in this file are the default parameters of each software/tool.

Ribodetector

  • -e norrna
    • norrna: output only high confident non-rRNAs, the rest are clasified as rRNAs;
  • --chunk_size 256:
    • chunk_size * 1024 reads to load each time.

fastp

  • -f 10
    • trimming how many bases in front for read1, default is 0 (int [=0])
  • -t 2
    • trimming how many bases in tail for read1, default is 0 (int [=0])
  • -q 15
    • the quality value that a base is qualified. Default 15 means phred quality >=Q15
  • -u 20
    • how many percents of bases are allowed to be unqualified (0~100). Default 40 means 40% (int [=40])
  • -n 0
    • if one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5 (int [=5])
  • -l 50
    • reads shorter than length_required will be discarded, default is 15. (int [=15]
  • -w 4
    • worker thread number, default is 2 (int [=2])

HISAT2

  • --dta -x
    • reports alignments tailored for transcript assemblers

samtools

  • -m 4G
    • Set maximum memory per thread; suffix K/M/G recognized [768M]
  • -@ 8
    • Number of additional threads to use [0]

gffread

  • -M
    • cluster the input transcripts into loci, discarding "redundant" transcripts (those with the same exact introns and fully contained or equal boundaries)
  • -K
    • for -M option: also discard as redundant the shorter, fully contained transcripts (intron chains matching a part of the container)
  • --table @geneid
    • output a simple tab delimited format instead of GFF, with columns having the values of GFF attributes given in ; special pseudo-attributes (prefixed by @) are recognized

trinityrnaseq

  • --seqType fq
    • sequence type, fastq or fasta
  • --est_method salmon
    • abundance estimation method. alignment_based:RSEM; alignment_free: kallisto|salmon
  • --thread_count 32
    • number of threads to use (default = 4)
  • --prep_reference
    • prep reference (builds target index)

blastp

  • -max_target_seqs 1
    • Maximum number of aligned sequences to keep (value of 5 or more is recommended) Default = `500'
  • -outfmt 6
    • alignment view options: 6 = Tabular
  • -evalue 1e-5
    • Expectation value (E) threshold for saving hits, Default = `10'

Trinotate: extract_GO_assignments_from_Trinotate_xls.pl

  • -G
    • gene-mode

BWA MEM

  • -T 19
  • -t 10

CIRI_AS

  • -D yes
    • if output all processing info (Choose 'yes' would require more disk space. default: no)