4 answers
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.
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)
You can also use transcripts(txdb) to get all transcript coordinates.
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
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written
by
Prakki Rama
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
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 - -
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
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