httools/config-Tf1.yaml at master · NICHD-BSPC/httools · GitHub

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# -----------------------------------------------------------
# Modify those parameters to match the samples
# -----------------------------------------------------------


# NOTE: this config file is in the YAML format, which does not allow the use of tabs.
# Two spaces are used instead for each indentation.


# Experiment name:
name: template_Tf1


# Indicate here the path(s) to the fastq(s), relative to the HTtools directory.
# If multiple files, indicate each file in its own line with an opening dash.

fastq:
  - test/SRR7068454full.fastq


# Sample blocks:
# Copy/paste the sample block for each of the samples in the library.
# Each block indicates:
#   - the sample name
#   - the barcode start position. Indicate 'none' for demultiplexed data
#   - the barcode length. Indicate 'none' for demultiplexed data
#   - the expected sequence from the barcode included to the end of LTR
#     (if the library has Serial Numbers, the SN can be indicated with Xs in the sequence.
#     Do not use A, T, G, C or N in the SN)
#   - integrase: whether a wild-type integrase (wt) or frameshift (fs) was used. This determines the
#     lenght of target site duplication (tsd). Only accepted values: wt or infs
#   - lib_design: from which end of the retrotransposon was the sequencing done?
#     Only accepted values: U5 or U3
#   - SN_position: position of the Serial Number. If no Serial Number, indicate 'none'
#   - SN_length: length of Serial Number. If no Serial Number, indicate 'none'


sample:
  # sample block ----------------------------------------------
  BC3498full:
    barcode_start: 1
    barcode_length: 4
    sequence: CTCACCGCAGTTGATGCATAGGAAGCCxxxxxxxxCAAACTGCGTAGCTAACA
    integrase: wt
    lib_design: U5
    SN_position: 28
    SN_length: 8
  # sample block ----------------------------------------------
  BC3512full:
    barcode_start: 1
    barcode_length: 4
    sequence: GTCACCGCAGTTGATGCATAGGAAGCCxxxxxxxxCAAACTGCGTAGCTAACA
    integrase: wt
    lib_design: U5
    SN_position: 28
    SN_length: 8
  # sample block ----------------------------------------------


# Genome built:
# Which genome built to use? Available options are:
#   - 1: Feb. 2007;
#   - 2: 2012 (ASM294v2);
#   - 3: Feb. 2007 + donor plasmid sequence;
#   - 4: 2012 (ASM294v2) + donor plasmid sequence (user)
genome: 2


# Generate fasta file(s) of trimmed sequence reads corresponding
# to the integration file
# Sequences are trimmed after the end of the LTR and replicated
# as many times as there was duplicate sequences.
# Set to True or False
generate_uncollapsed: True


# Positions to exclude:
# Indicate the list of position(s) to exclude, in the format
# chromosome_coordinate_orientation, i.e. chr1_240580_-
# Those positions will be screened out from the true_integrations
# and saved in location/excluded/ for reference
# Indicate 'none' if no position to exclude
exclude:
  - chr1_240580_-
  - chr1_54801_+


# -----------------------------------------------------------
# Advanced parameters
# -----------------------------------------------------------

# Those parameters do not typically need to be modified.
# Filters against linker, ltrcircle, plasmid, primary_incomplete,
# second_incomplete and pbs are optional. Indicate 'none' to skip
# those filters.

legacy_mode: False
length_to_match: 34
min_length: 14
allowed_mismatches: 2
linker: TAGTCCCTTAAGCGGAG
ltrcircle:
  U5: TGTCAGCAATACTAGCAGCATGGCTGATACACTA
  U3: TGTTAGCTACGCAGTTACCATAAACTAAATTCCT
plasmid:
  U5: GAAGTAAATGAAATAACGATCAACTTCATATCAA
  U3: none
primary_re:
  U5: MseI
  U3: MseI
primary_incomplete:
  U5: TTAA
  U3: TTAA
second_re:
  U5: SpeI
  U3: BspHI
second_incomplete:
  U5: AATTCTTTTCGAGAAAAAGGAATTATTGACTAGT
  U3: TTACATTGCACAAGATAAAAATATATCATCATGA
dist_to_second_incomplete:
  U5: 28
  U3: 22
pbs:
  U5: ATAACTGAACT
  U3: TTGCCCTCCCC
tsd:
  wt: 5
  infs: 0
blastview: 6
blastevalue: 0.05
max_score_diff: 0.0001
orf_map_interval: 100
avg_orf_length: 1500
orf_map_window: 5000
genomedb:
  1: database/2007/chr123.fas
  2: database/2012_ASM294v2/chr123.fas
  3: database/2007_with_pHL2882/chr123pHL2882.fas
  4: database/2012_ASM294v2_pHL2882/chr123pHL2882.fas
genomevs:
  1: v07str
  2: v12str
  3: v07pHL
  4: v12pHL
preexist_ltr:
  U5:
    ltr5: database/LTR_2012_ASM294v2/Tf2_5_LTR.txt
    ltr3: database/LTR_2012_ASM294v2/Tf2_3_LTR.txt
    sololtr: database/LTR_2012_ASM294v2/solo_LTR.txt
  U3:
    ltr5: database/LTR_2012_ASM294v2/Tf2_5_LTR-U3.txt
    ltr3: database/LTR_2012_ASM294v2/Tf2_3_LTR-U3.txt
    sololtr: database/LTR_2012_ASM294v2/solo_LTR-U3.txt
genomecds:
  1: database/2007/cds.txt
  2: database/2012_ASM294v2/cds.txt
  3: database/2007_with_pHL2882/cds.txt
  4: database/2012_ASM294v2_pHL2882/cds.txt

# List of chromosomes of interest
# The integration log file will give for infomration purpose the count within each chromosome
# in the reference genome, but only the chromosomes from the list below will be included
# in the output files integration, intergenic, ORF, location, ORFmap, logoDNA
chro_listvs:
  1: short_chro_list
  2: full_chro_list
  3: short_chro_list
  4: full_chro_list
full_chro_list:
  - chr1
  - chr2
  - chr3
  - AB325691
short_chro_list:
  - chr1
  - chr2
  - chr3