Is it possible to get .bed file of sequenced regions after NGS experiment?

Question

[Adam]

Hello,

As it is in post title, Is it possible to get .bed file of sequenced regions after NGS experiment? I mean that you have results of NGS experiment, let's take WES of 6 samples. Than I'd like to generate .bed file with regions of sequenced regions.

To be honest I need this to generate opportunity matrix which is created from those regions:

3.1 of below vignette https://www.bioconductor.org/packages/3.7/bioc/vignettes/signeR/inst/doc/signeR-vignette.html

Unfortunately I didn't recieve any of .bed files from the company that performed the experiment. All I got are .bam's.

In addition to this, can I take regions of coding sequences from UCSC's table browser?

Best regards, Adam

Answer 1

[Alex Reynolds]

You can use BEDOPS bam2bed:

$ bam2bed < reads.bam > reads.bed

Or BEDOPS convert2bed, to do the same thing:

$ convert2bed -i bam < reads.bam > reads.bed

If you have a bunch of BAM files in one directory and you're running bash:

$ for fn in `ls *.bam`; do bam2bed < ${fn} > ${fn%.*}.bed; done

To get coding sequences, you could download Gencode records and filter them for CDS entries (assuming hg38):

$ wget -qO- ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/gencode.v28.annotation.gff3.gz \
    | gunzip --stdout - \
    | awk '$3 == "CDS"' - \
    | convert2bed -i gff - \
    > CDS.bed

[Adam]

Amazing! That is what I need, many thanks!

[cpad0112]

Gencode latest release is 27, not 28 (as per URL available in my region- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/.

you can use parallel instead of loop:

$ parallel bam2bed {} {.}.bed ::: *.bam

[Alex Reynolds]

GNU Parallel is great, but it is IO limited when running on serial hardware.

[Alex Reynolds]

If you really want to take advantage of parallelization, and you have indexed BAM files, and you have a Slurm or SGE cluster, take a look at bam2bed_slurm or bam2bed_sge. Or, preferably, bam2starch_slurm or bam2starch_sge to make Starch archives.

[Alex Reynolds]

I fixed the link to the Gencode v28 URL.

[cpad0112]

URL fixed. Thanks.@Alex.

[Alex Reynolds]

BEDOPS and Unix streams are an awesome combination. Use them where you can!