Question

I have two tables. One is the “probe” and the other “transcript”.

Probe table: “probe”

ProbeID——-TranscriptID—-

2655       4555555
2600       5454542
2600       4543234
2344       5659595

…etc

Transcript table: “transcript”

TranscriptID—-Location—-

7896736      chr1
5454542      chr1

…etc

I need to find out how many transcripts per chromosome? AND How many probes per chromosome?

SELECT COUNT(*) 
FROM transcript

= ‘28869’ #Above I think gives me the transcripts per chromosome (i.e. location).

I need help with answering the second part (and first, if its wrong). I am assuming I need to use the JOIN clause.

Thank you.

Answer 1

Number of probes per chromosone

SELECT Location, COUNT(ProbeID) AS ProbeCnt
FROM transcript T
JOIN probe P ON P.TransciprtID = T.TranscriptID
GROUP BY Location
-- optionally you can ORDER BY to either get
-- ORDER BY COUNT(ProbID) DESC  --  list in descending order of nb of probes
-- ORDER BY Location            --  list in order of chromosome name

As to your first query it is incorrect. To get
the number of transcripts per chromosome, you need

SELECT Location, COUNT(TranscriptID) as TransCnt
FROM transcript
GROUP BY Location

Your current query gives the total number of transcripts for the whole transcript table, regardless of the chromosome.