How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
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Entering edit mode
8.3 years ago
pristanna ▴ 710

Hi everyone,

I need a bed file containing starts and ends of the exons, gene name and number of the exon - but just for the canonical transcript - because I don't want to have the regions repeated.

I tried UCSC Table browser and BioMart but non of them gives me exactly what I need.

Using UCSC I can get canonical transcripts (but at the same time I couldn't get starts and ends of the exon altogether with the gene name).

Using BioMart I can get starts and ends of the exons altogether with the gene name, but I can't find how to choose the canonical transcripts and that's why the regions are repeated as seen below in the case of NUS1P3:

Chromosome Name    Exon Chr Start (bp)    Exon Chr End (bp)    Associated Gene Name    Exon Rank in Transcript
1    955551  955753  AGRN    1
1    957579  957842  AGRN    2
1    970629  970730  AGRN    3
13     24902349    24903210    NUS1P3    1
13     24902376    24902559    NUS1P3    1
13  24902577    24902961    NUS1P3    2
13     24903006    24903210    NUS1P3    3


Thank you in advance for any suggestions!

bed transcript ucsc biomart • 34k views
0
Entering edit mode

Hello.

I would need to get a BED file with coordinates for each exon of the canonical RefSeq transcripts.

I tried the UCSC solution above but I understand that - UCSC known canonical transcripts do not necessarily correspond to RefSeq canonical (?) - I do not manage to get the information by exon (eg. NM_000xxx_exon1, NM_000xxx_exon2, ...).

As a second step, I would like to limit the gene content of my BED file to the gene list of the Clinical Genomic Database.

Could somebody help me with this ?

43
Entering edit mode
8.3 years ago
pristanna ▴ 710

Download a bed file for the canonical transcripts using UCSC Table Browser:

• track: UCSC Genes
• table: knownCanonical
• output format: select fields from primary and related tables
• press get output
• select fields from hg19.knownCanonical: chrom, chromStart, chromEnd,
• transcript select fields from hg19.kgXref: geneSymbol
• press get output

The file UCSC_canonical.bed looks like:

#hg19.knownCanonical.chrom      hg19.knownCanonical.chromStart  hg19.knownCanonical.chromEnd    hg19.knownCanonical.transcript  hg19.kgXref.geneSymbol
chr1    11873   14409   uc010nxq.1      DDX11L1
chr1    14361   19759   uc009viu.3      WASH7P
chr1    14406   29370   uc009viw.2      WASH7P
chr1    34610   36081   uc001aak.3      FAM138F
chr1    69090   70008   uc001aal.1      OR4F5
chr1    134772  140566  uc021oeg.2      LOC729737
chr1    321083  321115  uc001aaq.2      DQ597235
chr1    321145  321207  uc001aar.2      DQ599768
chr1    322036  326938  uc009vjk.2      LOC100133331


Download a bed file for all UCSC exons using UCSC Table Browser:

• track: UCSC Genes
• table: knownGene
• output format: BED - browser extensible data
• press get output
• select option Exons
• press get BED

The file UCSC_exons.bed looks like that:

chr1    11873   12227   uc001aaa.3_exon_0_0_chr1_11874_f        0       +
chr1    12612   12721   uc001aaa.3_exon_1_0_chr1_12613_f        0       +
chr1    13220   14409   uc001aaa.3_exon_2_0_chr1_13221_f        0       +
chr1    11873   12227   uc010nxr.1_exon_0_0_chr1_11874_f        0       +
chr1    12645   12697   uc010nxr.1_exon_1_0_chr1_12646_f        0       +
chr1    13220   14409   uc010nxr.1_exon_2_0_chr1_13221_f        0       +
chr1    11873   12227   uc010nxq.1_exon_0_0_chr1_11874_f        0       +
chr1    12594   12721   uc010nxq.1_exon_1_0_chr1_12595_f        0       +
chr1    13402   14409   uc010nxq.1_exon_2_0_chr1_13403_f        0       +
chr1    14361   14829   uc009vis.3_exon_0_0_chr1_14362_r        0       -


Modify the file to separate the transcript name of the rest of information:

awk '{split ($4,a,"_"); {print$1"\t"$2"\t"$3"\t"a[1]"\t"a[3]"\t"$6}}' UCSC_exons.bed > UCSC_exons_modif.bed  The file UCSC_exons_modif.bed: chr1 11873 12227 uc001aaa.3 0 + chr1 12612 12721 uc001aaa.3 1 + chr1 13220 14409 uc001aaa.3 2 + chr1 11873 12227 uc010nxr.1 0 + chr1 12645 12697 uc010nxr.1 1 + chr1 13220 14409 uc010nxr.1 2 + chr1 11873 12227 uc010nxq.1 0 + chr1 12594 12721 uc010nxq.1 1 + chr1 13402 14409 uc010nxq.1 2 + chr1 14361 14829 uc009vis.3 0 -  Join the sorted files based on the transcript identificator: join -1 4 -2 4 <(sort -k4 UCSC_exons_modif.bed ) <(sort -k4 UCSC_canonical.bed) | awk '{print$2"\t"$3"\t"$4"\t"$10"\t"$5"\t"$6}' | bedtools sort -i "-" > UCSC_exons_modif_canonical.bed  The final file contains exons of the canonical transcripts: chr1 11873 12227 DDX11L1 0 + chr1 12594 12721 DDX11L1 1 + chr1 13402 14409 DDX11L1 2 + chr1 14361 14829 WASH7P 0 - chr1 14406 16765 WASH7P 0 - chr1 14969 15038 WASH7P 1 - chr1 15795 15947 WASH7P 2 - chr1 16606 16765 WASH7P 3 - chr1 16857 17055 WASH7P 4 - chr1 16857 17055 WASH7P 1 -  ADD COMMENT 2 Entering edit mode At this step: transcript select fields from hg19.kgXref: geneSymbol, one need to check kgID in that hg19.kgXref table to produce the expected UCSC_canonical.bed. Another important thing: exon numeration is always forward! So if the gene is in reverse complement strand than Exon 0 there is the last exon. ADD REPLY 0 Entering edit mode Pulling this thread again since I got this error: header$ join -1 4 -2 4 <(sort -k4 UCSC_exons_modif.bed ) <(sort -k4 UCSC_canonical.bed) | awk '{print $2"\t"$3"\t"$4"\t"$10"\t"$5"\t"$6}' | bedtools sort -i "-" > UCSC_exons_modif_canonical.bed
join: /dev/fd/62:7064: is not sorted: chrX    155255322    155257848    DDX11L family member

0
Entering edit mode

Did you solve this issue?

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Entering edit mode

I found doing the following worked to reproduce the output as shown by pristanna, I made just one minor change to the method pristanna detailed:

Download a bed file for the canonical transcripts using UCSC Table Browser:

track: UCSC Genes table: knownCanonical output format: select fields from primary and related tables press get output select fields from hg19.knownCanonical: chrom, chromStart, chromEnd,transcript transcript select fields from hg19.kgXref: geneSymbol press get output

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Pulling this thread once again for a question:

Why the file "UCSC_canonical.bed" contains all the transcripts of a gene with multiple isoforms? Should'nt a canonical bed contain the "longest one" ? For example, here for the this gene "WASH7P", this file has 2 transcripts; uc009viu.3 and uc009viw.2. What I wanted (or I thought rather) is that it should have the canonical (which is mostly the longest; though there are varied views on that).

chr1    14361   19759   uc009viu.3      WASH7P
chr1    14406   29370   uc009viw.2      WASH7P


If it is expected to contain all the isoforms, then , is there any way from "UCSC" to get ONLY the longest one?

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I happened to write a custom python script to fetch the canonical transcript.

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There is a consequential error in you response.

- select fields from hg19.knownCanonical: chrom, chromStart, chromEnd,
- transcript select fields from hg19.kgXref: geneSymbol

Should be:
- select fields from hg19.knownCanonical: chrom, chromStart, chromEnd, transcript
- select fields from hg19.kgXref: geneSymbol

Once I figured that out, it worked perfectly. Thank you!

4
Entering edit mode
2.6 years ago
kdauria ▴ 40

To get directly from ensembl database...

mysql -h ensembldb.ensembl.org -u anonymous -P 3306 homo_sapiens_core_98_38

Then

SELECT DISTINCT
seq_region.name AS chrom,
exon.seq_region_start AS start,
exon.seq_region_end AS end,
gene_names.display_label AS gene_name,
exon_transcript.rank AS exon_number,
exon.seq_region_strand AS strand
FROM gene
JOIN transcript ON transcript.transcript_id = gene.canonical_transcript_id
JOIN exon_transcript ON exon_transcript.transcript_id = transcript.transcript_id
JOIN exon ON exon_transcript.exon_id = exon.exon_id
JOIN seq_region ON seq_region.seq_region_id = gene.seq_region_id
LEFT JOIN (
SELECT xref_id, display_label
FROM xref
WHERE xref.external_db_id = 1100
) AS gene_names ON gene_names.xref_id = gene.display_xref_id
WHERE gene_names.display_label = 'TP53' AND
LEFT(gene.stable_id, 4) <> 'LRG_'
ORDER BY seq_region.name, exon.seq_region_start;


Output for this example query:

+-------+---------+---------+-----------+-------------+--------+
| chrom | start   | end     | gene_name | exon_number | strand |
+-------+---------+---------+-----------+-------------+--------+
| 17    | 7668402 | 7669690 | TP53      |          11 |     -1 |
| 17    | 7670609 | 7670715 | TP53      |          10 |     -1 |
| 17    | 7673535 | 7673608 | TP53      |           9 |     -1 |
| 17    | 7673701 | 7673837 | TP53      |           8 |     -1 |
| 17    | 7674181 | 7674290 | TP53      |           7 |     -1 |
| 17    | 7674859 | 7674971 | TP53      |           6 |     -1 |
| 17    | 7675053 | 7675236 | TP53      |           5 |     -1 |
| 17    | 7675994 | 7676272 | TP53      |           4 |     -1 |
| 17    | 7676382 | 7676403 | TP53      |           3 |     -1 |
| 17    | 7676521 | 7676622 | TP53      |           2 |     -1 |
| 17    | 7687377 | 7687538 | TP53      |           1 |     -1 |
+-------+---------+---------+-----------+-------------+--------+
11 rows in set (6.66 sec)

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Entering edit mode
8.3 years ago

Perhaps apply a BEDOPS bedmap map operation, mapping BioMart-sourced exons to UCSC-sourced canonical transcripts. You could do something like:

$bedmap --echo --echo-map-id-uniq ucsc_canonical.sorted.bed biomart_exons.sorted.bed > answer.bed  The --echo operator prints each canonical element. The --echo-map-id-uniq operator prints the unique ID name(s) for exons whose genomic ranges span across the canonical element's genomic range. If you want all the exon information, ranges and all, use --echo-map in place of --echo-map-id-uniq. The default overlap criteria is one or more bases between map (exon) and reference (canonical) element - you can adjust this stringency up to complete overlap. It looks like you'd need to pre-process the BioMart data into UCSC BED format (renaming chromosomes, at least). Prepending the chromosome index with the string chr can be done with a simple awk statement: $ awk '{print "chr"$0}' biomart_stuff.bed > biomart_stuff_with_UCSC_chromosome_names.bed  If necessary, also sort the BED data: $ sort-bed ucsc_canonical.bed > ucsc_canonical.sorted.bed
\$ sort-bed biomart_exons.bed > biomart_exons.sorted.bed


Do this once, if your data are of uncertain sort order. This lets you take advantage of BEDOPS speed and memory enhancements. You only need to sort input sets once.

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Thanks a lot Alex for the idea, I am not familiar with BEDOPS, but I will try, it looks interesting!

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Let us know if you have any questions!

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Entering edit mode

Finally I solved it using different approach, but for another task I need some tool which can work with the overlap criteria, so I am going to try the BEDOPS now! Thanks a lot!