creating a matrix

[mictadlo]

The first is a reference file (chr03) which contains one long sequence (35020413 characters long) and the other file contained multiple sequences with different lengths and different ids (tig00007144, tig00026480,...). I used an alignment software called BLAST to align these two sequences. The original alignment results are stored in tab separated file:

tig00007144	chr03	23113	30824	33203431	33211142
tig00026480	chr03	1	48387	35010628	34962190
tig00003221	chr03	16916	29961	2127862	2140878
tig00010111	chr03	218	6989	23106738	23113500
tig00000318	chr03	1	18244	28621116	28639312
tig00009327	chr03	32147	40878	34160279	34151526
tig00025208	chr03	65878	79311	17006900	17020370
tig00019172	chr03	43720	50583	23113500	23106638
tig00004923	chr03	44154	50849	21159875	21153164

This is the column explanation:

• query_name = column 0
• subject_name = column 1
• query_start = column 2
• query_end = column 3
• subject_start = column 4]
• subject_end = column 5

I would like to see which parts (tig00007144, tig00026480, ...) mapping where to chr03.

Any idea how to create such matrix?

Thank you in advance.

Michal

[mbostock]

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