Chip-Seq And Ncrna ....

Question

[Hhgg]

I have a specific sequence that corresponds to a long ncRNA. This is its information:

                     /organism="Homo sapiens"
                     /mol_type="transcribed RNA"
                     /db_xref="taxon:9606"
                     /chromosome="12"
                     /map="12q13.13"

I also have chip-seq data for a HM. What Im trying to do is find the coverage of every nucleotide in my long ncRNA sequence from the chip-seq data. Based on the ChIP-seq data for the HM, I want to calculate the coverage of each nucleotide in my long ncRNA (number of reads that cover a nucleotide). How can i do that? I've never worked with chip-seq data before so any help would be greatly appreciated.

Answer 1

[David Langenberger]

If you are working with only one locus, I would do something like this:

samtools view -b mappedChipSeqData.bam chromosome:start-end > locus.unsorted.bam

samtools sort locus.unsorted.bam locus
samtools index locus.bam

samtools depth locus.bam

You can also try to call mpileup with -l and give it a bed-file containing your locus, then you can run it directly on the mappedChipSeqData.bam without creating this locus.bam.

[David Langenberger]

Of course, you have to map your ChipSeq data first! ;)