The position of the short read on genome

[zhenbinhu]

Hi all,
Do any one know how to get the position of the short read on genome?
Any advice about this would be much appreciated, thank you.

[Brian Bushnell]

The normal approach is to map it with a program such as BBMap.

[blancha]

Your question is extremely vague.

If you want to align millions of short reads to a reference genome, use TopHat or BBMap to map all the reads to a reference genome, as Brian Bushnell suggested.

The reference genomes can be downloaded from Ensembl or UCSC.

You can also use Galaxy if you are not comfortable using the Unix command line.

If you just want to align a single read, the UCSC Genome Browser has a convenient tool BLAT tool available online on the UCSC Genome Browser.

[zhenbinhu]

Sorry for vague question.
I have aligned million of short reads to a reference genome, but I don't know how to extract the position information for each short read.
Thanks for your advice, I will try as your advice.

[blancha]

Why would you want to extract the position information for each read?

If it's ChIP-Seq, you can use macs2 to call the peaks, and identify the positions of the peaks.

If it's RNA-Seq, you can use Cuffdiff or htseq-count and DESeq2 to count the number of reads for each gene annotated in the GTF file given.

I will try to answer your question exactly as you asked it though. Most mapping programs will generate SAM files or BAM files. The 3rd and 4th fields of each entry in the SAM file will contain the reference sequence name (chromosome) and the 1-based leftmost mapping position.

You can view the SAM format here.

http://samtools.github.io/hts-specs/SAMv1.pdf

You can convert BAM files to SAM files with samtools view.

[blancha]

IGV is also a useful option to visualize your alignment files.

https://www.broadinstitute.org/igv/