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View Process Hh 11

Cleaning and extraction of Ilumina reads from RNAseq output. Q20 Value.

jnun@tunebo:/data/process/Broca/Transcriptoma/Ensamblajes/CLCtranscriptomeHybri$ /opt/CLC/clc-assembly-
cell-4.0.1beta-linux_64/quality_trim -r ../../../BrocaRNASeq/Broca-RR.fq -o BrocaRR-Trim.fasta
Input reads: 10417004
Input residues: 510433196
Output reads: 9333846 89.60 %
Output residues: 437972812 85.80 %
Quality range: 2 to 40

jnun@tunebo:/data/process/Broca/Transcriptoma/Ensamblajes/CLCtranscriptomeHybrid /opt/CLC/clc-assembly-cell-4.0.1beta-linux_64/quality_trim -r ../../../BrocaRNASeq/Broca-SS.fq -o BrocaSS-trim.fasta
Input reads: 9991727
Input residues: 489594623
Output reads: 8979034 89.86 %
Output residues: 421926039 86.18 %
Quality range: 2 to 40

/opt/CLC/clc-assembly-cell-4.0.1beta-linux_64/quality_trim -r ../../BROCA_ESTs_crudos/HhaLPANor454.fasta -q ../../BROCA_ESTs_crudos/HhaLPANor454.qual -m 70 -o HhaLPANor454_trim.fasta &
Input reads: 175253
Input residues: 38026591
Output reads: 165570 94.47 %
Output residues: 35555536 93.50 %
Quality range: 6 to 40

/opt/CLC/clc-assembly-cell-4.0.1beta-linux_64/quality_trim -r ../../BROCA_ESTs_crudos/Hh_in.sanger.fasta -q ../../BROCA_ESTs_crudos/Hh_in.sanger.qual -m 70 -o Hh_in.sanger_trim.fasta &
Input reads: 4870
Input residues: 2238573
Output reads: 4325 88.81 %
Output residues: 1896920 84.74 %
Quality range: 3 to 60

/opt/CLC/clc-assembly-cell-4.0.1beta-linux_64/quality_trim -r ../../BROCA_ESTs_crudos/Plate_2_454.fasta -q ../../BROCA_ESTs_crudos/Plate_2_454.fasta.qual -m 70 -o Plate_2_454_trim.fasta &
Input reads: 484972
Input residues: 103689145
Output reads: 337364 69.56 %
Output residues: 68684372 66.24 %
Quality range: 0 to 40

/opt/tgicl_linux/bin/mdust BrocaRR-Trim.fasta > BrocaRR-Trim_mdust.fasta &

/opt/tgicl_linux/bin/mdust BrocaSS-trim.fasta > BrocaSS-Trim_mdust.fasta &

/opt/tgicl_linux/bin/mdust HhaLPANor454_trim.fasta > HhaLPANor454_trim_mdust.fasta &

/opt/tgicl_linux/bin/mdust Hh_in.sanger_trim.fasta > Hh_in.sanger_trim_mdust.fasta &

/opt/tgicl_linux/bin/mdust Plate_2_454_trim.fasta > Plate_2_454_trim_mdust.fasta &

/opt/CLC/clc-assembly-cell-4.0.1beta-linux_64/remove_duplicates -p -r BrocaRR-Trim_mdust.fasta -o BrocaRR-Trim_mdust_noDuplicates.fasta &

/opt/CLC/clc-assembly-cell-4.0.1beta-linux_64/remove_duplicates -p -r BrocaSS-Trim_mdust.fasta -o BrocaSS-Trim_mdust_noDuplicates.fasta &

/opt/CLC/clc-assembly-cell-4.0.1beta-linux_64/remove_duplicates -p -r HhaLPANor454_trim_mdust.fasta -o HhaLPANor454_trim_mdust_noDuplicates.fasta

/opt/CLC/clc-assembly-cell-4.0.1beta-linux_64/remove_duplicates -r Hh_in.sanger_trim_mdust.fasta -o Hh_in.sanger_trim_mdust_noDuplicates.fasta

/data/process/Broca/Transcriptoma/Ensamblajes/CLCtranscriptomeHybrid# time /opt/CLC/clc-assembly-cell-4.0.1beta-linux_64/clc_novo_assemble -o CLCtranscriptomeHybrid.fasta -q BrocaRR-Trim_mdust_noDuplicates.fasta BrocaSS-Trim_mdust_noDuplicates.fasta HhaLPANor454_trim_mdust_noDuplicates.fasta Hh_in.sanger_trim_mdust_noDuplicates.fasta Plate_2_454_trim_mdust_noDuplicates.fasta
Progress: 100.0 %
——-
real 11m29.659s
user 18m54.120s
sys 0m10.470s

bq. time /opt/CLC/clc-assembly-cell-4.0.1beta-linux_64/clc_ref_assemble_long -o CLCtranscriptomeHybrid.cas -d CLCtranscriptomeHybrid.fasta -q BrocaRR-Trim_mdust_noDuplicates.fasta BrocaSS-Trim_mdust_noDuplicates.fasta HhaLPANor454_trim_mdust_noDuplicates.fasta Hh_in.sanger_trim_mdust_noDuplicates.fasta Plate_2_454_trim_mdust_noDuplicates.fasta
Progress: 100.0 %
real 16m47.957s
user 13m30.900s
sys 0m14.560s

/opt/CLC/clc-assembly-cell-4.0.1beta-linux_64/sequence_info -n -r CLCtranscriptomeHybrid.fasta 

File                           CLCtranscriptomeHybrid.fasta

Number of sequences                 22243

Residue counts:
  Number of A's                   4063322   30.83 %
  Number of C's                   2512842   19.07 %
  Number of G's                   2509077   19.04 %
  Number of T's                   4058120   30.79 %
  Number of N's                     36155    0.27 %
  Total                          13179516

Sequence lengths:
  Minimum                             200
  Maximum                           16694
  Average                             592.52
  N50                                 763

Contig files:
    CLCtranscriptomeHybrid.fasta [ 22243 / 13179516 ]

  Read files:
    BrocaRR-Trim_mdust_noDuplicates.fasta [ 9297654 / 436236417 ]
    BrocaSS-Trim_mdust_noDuplicates.fasta [ 8866964 / 416538199 ]
    HhaLPANor454_trim_mdust_noDuplicates.fasta [ 161532 / 34750406 ]
    Hh_in.sanger_trim_mdust_noDuplicates.fasta [ 3421 / 1483071 ]
    Plate_2_454_trim_mdust_noDuplicates.fasta [ 227802 / 45935764 ]

Read info:

  Contigs                         22243
  Reads                        18557373
    Unmapped reads              1659280    8.94 %
    Mapped reads               16898093   91.06 %
      Multi hit reads            672818    3.98 %

Coverage info:

  Mapped nucleotides          834329956   89.24 %
  Total sites                  13179516
  Average coverage                   63.31

File:mapReadsWithAssembly.txt