number of exons

Question

[anba]

Hi,

I need to obtain list with four columns

gene_name genomic_length max_number_of_exons max_number_of_introns

and I can't find this information in aggegation format. I need to find the maximum number of exoms and introns for each gene.

I tried ensembl and uscs, and there is only information about number of transcripts, but I need the length and number of exon/introns. Where should I obtain such a list?

[WouterDeCoster]

Each gene has multiple transcripts which vary in length and or nu,ber of exons, so the table you describe either does not exist or is inherently incorrect.

[anba]

It seems that I write it unclear. I need the genomic length (not transcripts) and the maximum number of exons/introns for each gene. I've corrected my question.

[cpad0112]

$ awk '$3=="exon" && $2 == "BestRefSeq" {print}'  GRCh38_latest_genomic.gtf| gffread -F --keep-exon-attrs --table "gene_id","transcript_id",@numexons | sort -k1,1 | head -20

A1BG    NM_130786.4 8
A1BG-AS1    NR_015380.2 4
A1CF    NM_001198818.2  14
A1CF    NM_001198819.2  15
A1CF    NM_001198820.2  14
A1CF    NM_001370130.1  12
A1CF    NM_001370131.1  12
A1CF    NM_014576.4 13
A1CF    NM_138932.3 13
A1CF    NM_138933.3 13
A2M NM_000014.6 36
A2M NM_001347423.2  37
A2M NM_001347424.2  36
A2M NM_001347425.2  35
A2M-AS1 NR_026971.1 3
A2M-AS1 NR_137424.1 2
A2M-AS1 NR_137425.1 2
A2ML1   NM_001282424.3  25
A2ML1   NM_144670.6 36
A2MP1   NR_040112.1 9

You can take the maximum, from third column:

$ awk '$3=="exon" && $2 == "BestRefSeq" {print}'  GRCh38_latest_genomic.gtf| gffread -F --keep-exon-attrs --table "gene_id","transcript_id",@numexons | sort -k1,1 | datamash -sg1 max 3 | head

A1BG    8
A1BG-AS1    4
A1CF    15
A2M 37
A2M-AS1 3
A2ML1   36
A2MP1   9
A3GALT2 5
A4GALT  3
A4GNT   3

Answer 1

[Pierre Lindenbaum]

max number of exons per gene:

$ wget -q  -O - "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.txt.gz" | gunzip -c |\
    awk '{printf("%s\t%s\n",$13,$9);}' |\
    sort -t $'\t' -k1,1 -k2,2nr |\
    sort -t $'\t' -k1,1 -u --stable 

5S_rRNA 1
7SK 3
A1BG    8
A1BG-AS1    4
A1CF    15
A2M 36
A2M-AS1 3
A2ML1   36
A2ML1-AS1   2
A2ML1-AS2   2
A2MP1   9
A3GALT2 5
A4GALT  2
A4GNT   3
AAAS    16
AACS    18
AACSP1  11
AADAC   5
AADACL2 5
AADACL3 4
AADACL4 4
AADAT   14
AAED1   6
AAGAB   10
AAK1    22
AAMDC   7
AAMP    11
AANAT   7
AAR2    4
AARD    2

[cpad0112]

$ datamash -sg13 max 9 < wgEncodeGencodeBasicV19.txt | head -20

5S_rRNA 1
7SK 3
A1BG    8
A1BG-AS1    4
A1CF    15
A2M 36
A2M-AS1 3
A2ML1   36
A2ML1-AS1   2
A2ML1-AS2   2
A2MP1   9
A3GALT2 5
A4GALT  2
A4GNT   3
AAAS    16
AACS    18
AACSP1  11
AADAC   5
AADACL2 5
AADACL3 4