Detecting the peaks from RNAseq data

Question

[EVR]

Hi,

I have BAM file generated from RNAseq data and list of interesting regions for every scafold in genome. Now I would like to find the regions where peaks(based on width and depth) observed within the specified genomic regions. How could one can achieve it.

Thanks in advance

[GouthamAtla]

I understand that you have a list of regions in bed format scaffold_1 0 700 and the number of reads mapped to that region. Now you would like to filter regions based on the depth ? Is that correct ? Can you show few lines of data you have and what you would like to filter ?

Answer 1

[ivivek_ngs]

Do you have region of interest for which you want to intersect with your RNASeq data? If that is so then create normalized tracks or bedgraph files for both your RNASeq files and bed file of region of interest and charge them in UCSC or IGV browsers for the concerned genome assembly and try to visualize the regions that intersect be it at the exonic, intronic, intergenic regions. That is what I could make out from your question. You can always convert you aligned bams to bigbed or bed file and intersect with your specific regions of interest or even for that matter use bedtools that can intersect a bam file with known regions of interest in a bed file. This should be able to perform what you are looking for.

[EVR]

hi,

I already have the count data for the specified regions for every scaffold in genome. I would like find the region where the reads have been mapped. For an example, lets consider 200 reads were mapped to region 0-700 in scafold_1. Now when we visualize this region in IGV we found between 200 -270, theses 200 reads were dsitributed, I would like to extract this region 200-270 for scafold_1. Likewise I would like to extract regions where where reads have been mapped and peaks have been observed. Let me know if you need more details. kindly guide me

[ivivek_ngs]

I think I have missed out on something, since you are mentioning scaffold region then that means you are trying to denovo transcriptome assembly since usually scaffold regions contains contigs series for non-model organisms. So you have to follow tools that will specfically perform that task. Take a look at L_RNA_Scaffolder and see how it can be used for your purpose or even for that matter you can take a look at this publication.

Alternatively take a look at this tool as well

You can also take a look at this tool in github. They should perform the task you are trying to do.

You have to basically extract read coverage for scaffold regions from RNASeq data. That is what I understand.