Suggest Long Readings

This routine (which is available from the gap4 Experiments menu) suggests which templates could be resequenced on a long gel machine to fill in single stranded regions or extend contigs. The "Estimated long reading length" tells the routine the expected length of reading that will be produced by the sequencing machine. The routine finds all single stranded regions, and where possible suggests solutions. Solutions will not be suggested using readings from templates that have inconsistent read-pair information.

The example output below shows a list of problem segments followed by suggested templates.

  Prob 1..1:            Extend contig start for joining.
      Long       c91d3.s1   367. T_pos=366, T_size=1000..1500 (1250), cov 189
      Long      c99e12.s1   340. T_pos=191, T_size=1000..1500 (1250), cov 216

  Prob 1..456:          No +ve strand data.
      No solution.

  Prob 1597..1736:      No +ve strand data.
      Long       c53c6.s1  1074. T_pos=341, T_size=1000..1500 (1250), cov 32
      Long      e04c11.s1  1076. T_pos=376, T_size=1000..1500 (1250), cov 34
      Long       e05h9.s1  1081. T_pos=377, T_size=1000..1500 (1250), cov 39
      Long       e05a1.s1  1198. T_pos=329, T_size=1000..1500 (1250), cov 156*
      Long      c53b11.s1  1382. T_pos=216, T_size=1000..1500 (1250), cov 340*

  Prob 2530..2532:      No +ve strand data.
      Long       e03a8.s1  2283. T_pos=199, T_size=1000..1500 (1250), cov 308*
      Long      e05b10.s1  2331. T_pos=200, T_size=1000..1500 (1250), cov 356*

  Prob 3974..4067:      No -ve strand data.
      No solution.

  Prob 4067..4067:      Extend contig end for joining.
   D  Long       e06a3.s1  3588. T_pos=366, T_size=1000..1500 (1582), cov 76
      Long       c53b1.s1  3709. T_pos=360, T_size=1000..1500 (1250), cov 197

Some brief notes on the above output; looking at the suggested rerun of reading e05a1.s1.

Prob 1597..1736: No +ve strand data.

A single stranded region has been identified in this contig at bases 1597 to 1736 inclusive.

"?D Long"

The optional two letters before the word "Long" are used to flag possibly inconsistent templates (templates that are definitely inconsistent are ignored). "?" means that no primer information is available for the template that the reading is from. "D" means that the template size is not within the expected minimum and maximum. In this case the observed size is displayed (see below).

"Long e05a1.s1 1198."

A possible solution; rerun reading e05a1.s1 as a long gel. The first used base at the 5' end of this reading is at position 1198 in the contig. Typically this roughly corresponds to the primer position for this reading in the contig.

T_pos=329

The last used base at the 3' end of the reading is estimated to be the 329th base of the template. Together with the template lengths this gives us an estimate of how much template there is available for a long gel or for walking.

T_size=1000..1500 (1250)

The estimated size for this template is 1250 bases. Gap4 is supplied a minimum and maximum size when a reading is assembled. In this case the minimum is 1000 bases, and the maximum 1500. When forward and reverse reads assembled into the same contig estimate the real length reasonably accurately. Otherwise (as can be seen here), the estimated length is simply the average of the supplied minimum and maximum lengths.

cov 156*

We would expect a long gel to cover our "hole" by 156 bases. This estimate is based purely on the position of the start of the reading in relation to the start of the hole, and the estimated length of a long gel. The asterisk here marks that this coverage is more than enough to completely solve the problem by plugging the positive strand hole.

For the problem "3974..4067" there is "No solution" listed. This is due to the fact that there are no suitable readings within the estimated long gel reading length of this problem.