Extract depth coverage of a particular region from BAM file

Question: Extract depth coverage of a particular region from BAM file

2.4 years ago by

kuick77 • 10 wrote:

Hi, If any kind soul could help,

I loaded BAM files in IGV and i notice some interesting splicing junction read depth across my samples. I am currently manual click the location in order to view the depth. Is there a method to do that automatically to look at all junction coverage? I am working on targeted sequencing of exon junctions. I am particularly interested to extract the info e.g. 3045666 - 3045888 (genomic coordinate), depth = 456 which it will show when I click the splicing coverage region in IGV.

Many thanks

bam • 3.4k views

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modified 2.4 years ago • written 2.4 years ago by kuick77 • 10

2.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Several tools in the groups BEDTools, NGS: DeepTools, plus the tool NGS: RNA Analysis > htseq-count all perform coverage calculations for BAM datasets. Each does this slightly differently - review the tool forms to pick the one right for you.

If needed, the output can be post-filtered. Try Select or Filter.

There are many ways to do this, with different input requirements/settings and result output formats, so I don't want to limit you by giving just one choice. But, if you want to post back which tool you decided on (and why, including your specific analysis inputs and output choices), that would probably be useful to other Galaxy users reading here at Biostars.

Hopefully this helps! Jen, Galaxy team

ADD COMMENT • link written 2.4 years ago by Jennifer Hillman Jackson ♦ 25k

2.4 years ago by

kuick77 • 10

kuick77 • 10 wrote:

Hi Jen,

Thanks very much. screen shot

I attached the scenario.

I tried HTseq-count, but it requires a GFF file, I do not know about how to get it in order to complete the analysis.

Screen Shot

ADD COMMENT • link written 2.4 years ago by kuick77 • 10

2.4 years ago by

kuick77 • 10

kuick77 • 10 wrote:

I tried a simple method to achieve what i wanted, because personally I am not a bioinformatician.

What I did was:

1: Load the BAM file into IGV screen shot 2: Check "Show Splice Junction Track" 3. Right Click the splicing junction and click "Export Features" in bed file 4. Load the Bed file back to Galaxy 5. View the bed file and you will get and reads vs coordinates you want. 6. Then I manipulate the data in excel.

ADD COMMENT • link written 2.4 years ago by kuick77 • 10

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