Editing BioMicroCenter:IlluminaDataPipeline (section)

== Output Files ==

<B>_sequence.txt</B><br>
Fastq format sequence information
Example File:

 @HWI-EAS413_4:1:5:1004:56            <= Sequence name - lane:read(1|2):tile:X:Y
 GTTTCATTTCTAAACCTGTTTCATTACAAAATGCC  <= Sequence
 +HWI-EAS413_4:1:5:1004:56            <= repeat of name
 ZVZZVZZZZZVZSZZLZFZZZVVZLSZSZZQVLVT  <= ASCII quality score. A = low, Z(or other symbol) = high.
 @HWI-EAS413_4:1:5:1350:118
 GACCTTTTGCTTGTTTTGAGAGTGAGGGAAAAGGA
 +HWI-EAS413_4:1:5:1350:118
 ZZZZZZZZZZZZZZZZZYZZZUZZZYZUZUVVVSV

'''_export.txt and _sorted.txt'''
Export.txt files include all clusters. Sorted.txt file includes only reads passing filter and mapping uniquely to the genome.

 HWI-EAS413      24      8       82      1319    1073    0       1       AACTGCCAGTTGTGCCAGCTCCATTTTGAAAAAGG     a`a`_``W]Y^_Y]a][\_]__^\^_\^VY^Z\^Y     chr10.fa3004659 F       35      5   
 HWI-EAS413      24      8       30      1221    382     0       1       TCCACAAAATAGAAGCAGAAGGGACTCTACCCTTC     abbbbbabbb_b^`bbab`_a`aabaaabaaaaaa     chr10.fa3005954 R       35      11
 HWI-EAS413      24      8       66      1593    1942    0       1       TCCAGAGCCTGATGCTCGTCACAACTCTGCTCACT     abab[`[aa_aa[Ua[_PTaaaa\\YZTRXU`[[U     chr10.fa3012198 R       35      112
 HWI-EAS413      24      8       74      745     561     0       1       AGTCTCTGCTCCATTTTCATCCCTGCATTTCCTTT     abbbbbbbbbbaZabbba^aaababaaabaaaaab     chr10.fa3020132 R       35      15
 HWI-EAS413      24      8       65      1587    440     0       1       AGTCATCCATCTGAGAACACCTTCCAGGTCCTGGA     `]`baabba`ba_a^_Za_ba_aaa][XUba_TZY     chr10.fa3023984 R       35      67
 HWI-EAS413      24      8       99      224     363     0       1       TGTGTAATGCCCAAATATCAGTTCTAAATAGGTCA     aa`a``_aaaaa^^^`Z``^a_`_`YWW_W``]_X     chr10.fa3026498 F       35      113
 HWI-EAS413      24      8       15      1636    1926    0       1       AAACATTTATGAAATTGTCAAAGAACAAAAAACAA     aaaaaaaaaaaaaaaaa_a__^a_a``^_a````X     chr10.fa3026790 F       35      52
 HWI-EAS413      24      8       33      622     1685    0       1       AAACATTTATGAAATTGTCAAAGAACAAAAAACAA     aababaaabaaaaaaaa^aaaaa`a`a`aaa``aa     chr10.fa3026790 F       35      53
 HWI-EAS413      24      8       84      237     1877    0       1       AAACATTTATGAAATTGTCAAAGAACAAAAAACAA     ^aaababa_aabaaaaaaaa^R^`aaaaaaaa_aa     chr10.fa3026790 F       35      39
 HWI-EAS413      24      8       60      1470    635     0       1       TCGTGACGAGTAAAGCAGTCTCTCTTAGCTCTGTC     aba^`bb``a`_P`^]XX[aaa`a`]]U``a\TT_     chr10.fa3031823 F       35      113

FIELDS
# Machine (Parsed from Run Folder name)
# Run Number (Parsed from Run Folder name)
# Lane
# Tile
# X Coordinate of cluster
# Y Coordinate of cluster
# Index string (Bland for a non-indexed run)
# Read number (1 or 2 for paired-read analysis, blank for a single-read analysis)
# Read
# Quality string—In symbolic ASCII format (ASCII character code = quality value + 64. B-F = low)
# Match chromosome—Name of chromosome match OR code indicating why no match resulted
# Match Contig—Gives the contig name if there is a match and the match chromosome is split into contigs (Blank if no match found)
# Match Position—Always with respect to forward strand, numbering starts at 1 (Blank if no match found)
# Match Strand—“F” for forward, “R” for reverse (Blank if no match found)
# Match Descriptor—Concise description of alignment (Blank if no match found). A numeral denotes a run of matching bases and a letter denotes substitution of a nucleotide. For a 35 base read, “35” denotes an exact match and “32C2” denotes substitution of a “C” at the 33rd position
# Single-Read Alignment Score—Alignment score of a single-read match, or for a paired read, alignment score of a read if it were treated as a single read. Blank if no match found; any scores less than 4 should be considered as aligned to a repeat
# Paired-Read Alignment Score—Alignment score of a paired read and its partner, taken as a pair. Blank if no match found; any scores less than 4 should be considered as aligned to a repeat
# Partner Chromosome—Name of the chromosome if the read is paired and its partner aligns to another chromosome (Blank for single-read analysis)
# Partner Contig—Not blank if read is paired and its partner aligns to another chromosome and that partner is split into contigs (Blank for single-read analysis)
# Partner Offset—If a partner of a paired read aligns to the same chromosome and contig, this number, added to the Match Position, gives the alignment position of the partner (Blank for single-read analysis)
# Partner Strand—To which strand did the partner of the paired read align? “F” for forward, “R” for reverse (Blank if no match found, blank for single-read analysis)
# Filtering—Did the read pass quality filtering? “Y” for yes, “N” for no

'''''_eland_results.txt'''''<br>'''obsolete!'''
Alignment information for reads.

 <B>Sequence ID                     Sequence Read                           SCORE   #0mm    #1mm    #2mm   CHR HIT    POS HIT         STRND     unk.   MISMATCH</B><br>
 >HWI-EAS413_4:1:100:825:1989    CTAGAAGCAGAAGCAGGTATTTGGGGGGAGGGTTG     R0      3       0       0
 >HWI-EAS413_4:1:100:1076:1671   AACTGCTTTGAGATAGGGTCTCTCTTGTTCACTTT     NM      0       0       0
 >HWI-EAS413_4:1:100:573:1957    TCGAGACGTAAACTAGCTAACCTACATTATCCCCT     NM      0       0       0
 >HWI-EAS413_4:1:100:1784:660    AATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA     R0      204     255     255
 >HWI-EAS413_4:1:100:133:987     CGCGATGATGTCTCAATACACCCCCCCGCTACCAG     NM      0       0       0
 >HWI-EAS413_4:1:100:1361:1636   CATGTCATGCGCTCTAATCTCTGGGCATCTTGAGA     NM      0       0       0
 >HWI-EAS413_4:1:100:1733:932    CCGAACTTCTGACAGGTTTGAGCCTTCTGCTCAAG     U1      0       1       0       chr9.fa     110761807       F       DD      13A
 >HWI-EAS413_4:1:100:992:1902    CAATTAAATAATAATAAACTAACACACAATACAAA     NM      0       0       0
 >HWI-EAS413_4:1:100:1230:1718   TCAGCAAACAAACCCCCAACATAAAATCCATTATG     NM      0       0       0
 >HWI-EAS413_4:1:100:324:130     TCATCGAGAGGGGACTGAAGTGGAAGCTAGTCAGC     U0      1       0       0       chr14.fa    33191761        F       DD

Sequence ID: From the sequence.txt file<br>
Sequence Read: self explanatory<br>
Score: 8 possible scores:
* U0,U1,U2 - unique hit in the genome with 0, 1, or 2 mismatches
* R0,R1,R2 - multiple hit in the genome with 0, 1, or 2 mismatches
* NM - No match
* QC - failed quality score
0,1,2mm: Number of times the sequence was found in the genome with 0, 1 or 2 mismatches. max=255 <br>
Chr/Pos Hit: Location of the read in the genome (low number based on 36nt). Only reported for U0, U1, U2.<br>
Strand: Strand hit (F or R) ''Note: a hit a pos 1000 with a R actually has its 5' end at 1035!''<br>
Mismatch: Position of the mismatch (eg 13A = pos13 should be an A). listed as in sequence.<br>

'''''_realign.txt'''''<BR>'''obsolete!'''
Final quality-filtered sequence alignments

 '''sequence read                       score #hit  Chr:Pos      Strd  best match                         next best score'''
 CCACAAAGTTCAGATGAGGGTGGGTGTTGCTTGTT 17500 1     chrX:116488401  F CCACAAAGTTCAGATGAGGGTGGGTGTTGCTTGTT 14359
 AGACTGGCCTGCCTCTGCCTCCTGAGTACTGAGAC 17500 1     chr8:73831045   R GTCTCAGTACTCAGGAGGCAGAGGCAGGCCAGTCT 16453
 CTTGGGCTACCAGGCCTGGTTAGCCCACTCCCGCT 17500 1     chrX:95524949   R AGCGGGAGTGGGCTAACCAGGCCTGGTAGCCCAAG 14359
 CAGAAAGGAGCAAGAATCCGCTAAGCAGGGCCGGG 17500 1     chr11:119057429 R CCCGGCCCTGCTTAGCGGATTCTTGCTCCTTTCTG 14359
 ACTATTTCACAAAATAGAAGTAGAAGGTACTCTAC 17500 255
 GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTAGC 0     0
 CTATTGTGAATCATACTTCAATGAACATGAGTATG 0     0
 CTAGAAGCAGAAGCAGGTATTTGGGGGGAGGGTTG 17500 3
 CCGAACTTCTGACAGGTTTGAGCCTTCTGCTCAAG 16453 1     chr9:110761807  F CCGAACTTCTGAAAGGTTTGAGCCTTCTGCTCAAG 14359
 TCATCGAGAGGGGACTGAAGTGGAAGCTAGTCAGC 17500 1     chr14:33191761  F TCATCGAGAGGGGACTGAAGTGGAAGCTAGTCAGC 14359