Inconsistent query coordinates between chain and net alignments (Mm10 VS proCap1)

[Guillaume L]

Hi all,

In short:

I wonder why the query (proCap1) coordinates are not the same in net alignments and in chain alignments (looking at the same chainId).

In more details:

I tried to find the homologous genomic sequence of one gene (SMCHD1) in the rock hyrax (procavia Capensis). Unfortunately several hyrax contig are aligned to the mouse region (chr17:71344493-71475343) and I would like to retrieve a (hypothetical) continuous sequence.

Doing my request in the mysql database, I noticed that coordinates of fragments in proCap1 weren't the same, for a same "chainId" between the chain and net tables.

Here are my requests:

    use mm10;

    # Chain

    SELECT tName,tStart,tEnd,qStrand,qName,qStart,qEnd,score,id FROM chainProCap1

    WHERE (tName="chr17"

        AND (71344493 <= tStart AND tStart <= 71475343

            OR 71344493 <= tEnd AND tEnd <= 71475343))

    ORDER BY tStart;

    

    # Net

    SELECT level, tName,tStart,tEnd,strand,qName,qStart,qEnd,score,chainId FROM netProCap1

    WHERE (tName="chr17" AND type="top"

        AND (71344493 <= tStart AND tStart <= 71475343

            OR 71344493 <= tEnd AND tEnd <= 71475343))

    ORDER BY tStart;

I am not going to show the entire output here (18 and 19 rows), just the first row of each:

# Chain:

tName | tStart   | tEnd     | qStrand | qName           | qStart | qEnd   | score | id

chr17 | 71344307 | 71345537 | -       | scaffold_115863 |   4129 |   5390 | 33044   | 98261

# Net 

level | tName | tStart   | tEnd     | strand | qName           | qStart | qEnd   | score | chainId

1 | chr17 | 71344307 | 71345537 | -      | scaffold_115863 |    270 |   1531 | 33044 |   98261

This is the same piece of alignment in both cases, why are *qStart* and *qEnd* not matching?

Thanks in advance for your help. I realize I should probably use the .axt alignment, but now these different coordinates are puzzling me.

PS: If you want (a bit) more details, I asked the same question here, with the complete output : https://www.biostars.org/p/244058/

Best regards,

Guillaume

[Cath Tyner]

Hello Guillaume,

Thank you for contact the UCSC Genome Browser support team.

In short, chain and net tables use different conventions for representing query coordinates for opposite-orientation alignments; net uses coordinates from the forward strand of the query and chain uses coords from the reverse strand of the query. Each chain includes a sequence of aligned blocks. In order to list the target and query blocks in the same order, and still have ascending start coords in each list, we have to use query reverse strand coords. This isn't necessary for the net format; we can use "+" strand query coords because the net format has nested "fill" and "gap" elements that each have a single start and end in both target and query.

Below, we are looking at the scaffold_115863 in hyrax. The entire scaffold is 5,660 bp.

scaffold_115863 
pos1 (5')..........................................................pos5660 (3') 

NET " + " coords
(start)|............[270 (A)-----1531 (B)]..............................| (end) 

CHAIN " - " coords
(end)|..............[5390 (C)----4129 (D)]..............................| (start) 

scaffold_115863 reverse orientation
pos5660 (3')............................................................pos1 (5')

If you start counting from the left of the scaffold, you count 270 bp to the start A or C. If you start counting from the right, you count 5390 bp to reach A or C.
If you start counting from the left of the scaffold, you count 4129 bp to B or D. If you start counting from the right, you count 1531 bp to reach B or D.
Genomic size is the same for these regions, 5660bp.

Note that these coords can be transformed back and forth by subtracting from the query sequence length:

5660 - 270 = 5390
5660 - 1531 = 4129

Please respond to this list if you have further questions!

Thank you again for your inquiry and for using the UCSC Genome Browser. 

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. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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