The clc_mapping_table Program

The clc_mapping_table program takes a single cas file as input and prints assembly information for each read. By default, clc_mapping_table makes a table with one read per row. The columns are:

Read number (starting from 0).
Read name (enable using the `-n' option).
Read length.
Read position for alignment start.
Read position for alignment end.
Reference sequence number (starting from 0).
Reference position for alignment start.
Reference position for alignment end.
Whether the read is reversed (0 = no, 1 = yes).
Number of optimal locations for the read.
Alignment score (enable using the `-s' option).

If a read does not match, all columns except the read number and name are `-1'. If a read is reverse, the read positions for the alignment start and end are given after the reversal of the read. The sequence positions start from 0 indicating before the first residue and end at the sequence length indicating after the last residue. So a read of length 35, which matches perfectly will have an alignment start position of 0 and an alignment end position of 35.

Here is part of an example output using both the `-n' and the `-s' option:

208       SLXA-EAS1_89:1:1:622:715/1       35    0   35    0     89385     89420  0   1  35
209       SLXA-EAS1_89:1:1:622:715/2       35    0   35    0     89577     89612  1   1  35
210       SLXA-EAS1_89:1:1:201:524/1       35    0   32    0      4829      4861  0   1  29
211       SLXA-EAS1_89:1:1:201:524/2       -1   -1   -1   -1        -1        -1 -1  -1  -1
212       SLXA-EAS1_89:1:1:662:721/1       35    0   35    0     38254     38289  1   1  35
213       SLXA-EAS1_89:1:1:662:721/2       35    0   35    0     38088     38123  0   1  32
214       SLXA-EAS1_89:1:1:492:826/1       35    0   35    0     81872     81907  1   1  35
215       SLXA-EAS1_89:1:1:492:826/2       35    0   35    0     81685     81720  0   1  35

As the read names indicate, the data are from a paired experiment. Read 211 does not match at all and only the first 32 out of the 35 positions in read 210 matches. The score for this read is 29, indicating that a mismatch is also present (31 - 2 = 29). Read 213 also has a mismatch while the rest of the sequences match perfectly. We can also see that the pairs are located close together and on opposite strands.

Use the `-a' option to get a very detailed output (`-n' and `-s' are without effect here):

SLXA-EAS1_89:1:1:622:715/1 has 1 match with a score of 35:
      89385 TTGCTGTGGAAAATAGTGAGTCATTTTAAAACGGT 89419      coli
            |||||||||||||||||||||||||||||||||||
            TTGCTGTGGAAAATAGTGAGTCATTTTAAAACGGT            read
SLXA-EAS1_89:1:1:622:715/2 has 1 match with a score of 35:
      89577 AAACTCCTTTCAGTGGGAAATTGTGGGGCAAAGTG 89611      coli
            |||||||||||||||||||||||||||||||||||
            AAACTCCTTTCAGTGGGAAATTGTGGGGCAAAGTG            reverse read
SLXA-EAS1_89:1:1:201:524/1 has 1 match with a score of 29:
       4829 ATCCAGGCGAATATGGCTTGTTCCTCGGCACC    4860       coli
            ||||||||||||||||||| ||||||||||||
            ATCCAGGCGAATATGGCTTTTTCCTCGGCACCCCG            read
SLXA-EAS1_89:1:1:201:524/2 has 0 matches
SLXA-EAS1_89:1:1:662:721/1 has 1 match with a score of 35:
      38254 AGGGCATTCGATACGGTGGATAAGCTGAGTGCCTT 38288      coli
            |||||||||||||||||||||||||||||||||||
            AGGGCATTCGATACGGTGGATAAGCTGAGTGCCTT            reverse read
SLXA-EAS1_89:1:1:662:721/2 has 1 match with a score of 32:
      38088 ACTGAGTGATTGATTCGCGAGCCACATACTGTGGA 38122      coli
            |||||||||||||||||||||||||||||| ||||
            ACTGAGTGATTGATTCGCGAGCCACATACTCTGGA            read
SLXA-EAS1_89:1:1:492:826/1 has 1 match with a score of 35:
      81872 GCATCCAGCACTTTCAGCGCCTGGGTCATCACTTC 81906      coli
            |||||||||||||||||||||||||||||||||||
            GCATCCAGCACTTTCAGCGCCTGGGTCATCACTTC            reverse read
SLXA-EAS1_89:1:1:492:826/2 has 1 match with a score of 35:
      81685 TTCTGGTTGCTGGTCTGGTGGTAAATGTTCCCACT 81719      coli
            |||||||||||||||||||||||||||||||||||
            TTCTGGTTGCTGGTCTGGTGGTAAATGTTCCCACT            read

Note! The positions in the standard output assumes the reference sequence starts at 0. However, the `-a' option assumes that the reference starts at 1. This is due to the fact that the `-a' option is intended to produce human-readable output whereas the standard option is intended to be used by computer programs.

If multiple hit positions are recorded in the cas file (using the -t option when running the assembly), running the assembly_ table with the `-m', the output looks like this:

480         35    0   35    0     19625     19660  0   1
481         35    0   35    0     19815     19850  1   1
482         35    0   35    0   2512501   2512536  1   3
-           35    0   35    0    607436    607471  1   3
-           35    0   35    0     15593     15628  1   3
483         35    0   35    0   2512321   2512356  0   3
-           35    0   35    0    607256    607291  0   3
-           35    0   35    0     15413     15448  0   3
484         35    0   35    0     14374     14409  1   1
485         35    0   35    0     14194     14229  0   1

Reads 482 and 483 map in three places and they are all printed. The order is random, which has the advantage that using the first match (according to output order) is the same as using a random match. For paired data (like these), the matches are in the same order for two paired reads. So the first match for 482 belongs with the first match for 483, etc.

For alignment output in clc_mapping_table with "-m", it looks like this:

SLXA-EAS1_89:1:1:980:945/1 has 1 paired match with a score of 35: (alignment 1)
      19626 AGCTCCCCCAAAGTTAAGGTGGGGGAGATAGATTA 19660      coli
            |||||||||||||||||||||||||||||||||||
            AGCTCCCCCAAAGTTAAGGTGGGGGAGATAGATTA            read
SLXA-EAS1_89:1:1:980:945/2 has 1 paired match with a score of 35: (alignment 1)
      19816 GATAGTGTTTTATGTTCAGATAATGCCCGATGACT 19850      coli
            |||||||||||||||||||||||||||||||||||
            GATAGTGTTTTATGTTCAGATAATGCCCGATGACT            reverse read
SLXA-EAS1_89:1:1:307:821/1 has 3 paired matches with a score of 35: (alignment 1)
    2512502 CGGCCCCGGGGGGATGTCATTACGTGAAGTCACTG 2512536    coli
            |||||||||||||||||||||||||||||||||||
            CGGCCCCGGGGGGATGTCATTACGTGAAGTCACTG            reverse read
SLXA-EAS1_89:1:1:307:821/1 has 3 paired matches with a score of 35: (alignment 2)
     607437 CGGCCCCGGGGGGATGTCATTACGTGAAGTCACTG 607471     coli
            |||||||||||||||||||||||||||||||||||
            CGGCCCCGGGGGGATGTCATTACGTGAAGTCACTG            reverse read
SLXA-EAS1_89:1:1:307:821/1 has 3 paired matches with a score of 35: (alignment 3)
      15594 CGGCCCCGGGGGGATGTCATTACGTGAAGTCACTG 15628      coli
            |||||||||||||||||||||||||||||||||||
            CGGCCCCGGGGGGATGTCATTACGTGAAGTCACTG            reverse read
SLXA-EAS1_89:1:1:307:821/2 has 3 paired matches with a score of 35: (alignment 1)
    2512322 GGTATTACGCCTGATATGATTTAACGTGCCGATGA 2512356    coli
            |||||||||||||||||||||||||||||||||||
            GGTATTACGCCTGATATGATTTAACGTGCCGATGA            read

Options for the clc_mapping_table are described in Options for All Programs.

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The clc_mapping_table Program