list of gene or transcript IDs and their length

Question

[zizigolu]

Hi,

How I can get a list of gene or transcript IDs and their length in Saccharomyces cerevisiae please?

Thank you

Answer 1

[EagleEye]

A: Converting gtf format to bed format

If you have GTF file from gencode, above mentioned shell script should work in both gene level and transcript level.

[zizigolu]

yes, right, gtf file contains both

Answer 2

[zizigolu]

with featurecounts using bam and gtf file we can get the all of gene IDs and the length but i should select coding genes among them

Answer 3

[trausch]

In R using Bioconductor this should work (for ENSEMBL genes):

> library(GenomicAlignments)
> library(TxDb.Scerevisiae.UCSC.sacCer3.ensGene)
> txdb = TxDb.Scerevisiae.UCSC.sacCer3.ensGene
> txlen = transcriptLengths(txdb, with.utr5_len=TRUE, with.utr3_len=TRUE)
> head(txlen)

[Giovanni M Dall'Olio]

You can also use transcripts(txdb) to get all transcript coordinates.

[zizigolu]

thank you for your answer

Answer 4

[Prakki Rama]

From ENSEMBL

ftp://ftp.ensembl.org/pub/release-83/fasta/saccharomyces_cerevisiae/cds/

From NCBI - RefSeq

paste "Saccharomyces cerevisiae"[porgn:__txid4932] in NCBI browser. Select mRNA and RefSeq for list of genes from the left side menu.

Below the search bar, click Send to, Choose destination: File, Format as: Fasta

Sequences length - You can get sequences length using a AWK oneliner:

awk '/^>/ {if (sqlen){print sqlen}; print ;sqlen=0;next; } { sqlen = sqlen +length($0)}END{print sqlen}' file.fa

[zizigolu]

thank you very much,

I need transcript or gene IDs and the length and I don't need the fasta sequence of them

something like below I need

genesID geneslength
R0010W  1272
R0020C  1122
R0030W  546
R0040C  891
YAL069W  315

but NCBI-refseq only has 8 IDs

[Prakki Rama]

Check this screenshot of what I see in NCBI gene list for Saccharomyces cerevisiae -

Once you download

awk '/^>/ {if (sqlen){print sqlen}; print ;sqlen=0;next; } { sqlen = sqlen +length($0)}END{print sqlen}' filename.fa | paste - -

[zizigolu]

thank you for paying attention,

I mapped my reads on cdna instead of genome fasta with bowtie2 then I need something like all of coding sequend IDs and their length

what I got with your kindly tip is like below

>gi|891176844|ref|NM_001305015.2| Saccharomyces cerevisiae S288c hypothetical protein partial mRNA
5410
>gi|891176612|ref|NM_001310667.1| Saccharomyces cerevisiae S288c hypothetical protein partial mRNA
333