Question: bedtools genomecov per-base report in igv
0
gravatar for pyKey
11 months ago by
pyKey50
pyKey50 wrote:

Hi All,

Is there a way to transform the per-base report of an alignment file into igv-readable format? Original command:

bedtools genomecov -d -ibam sample_file > out_file

Thank you,

igv per-base report bedtools • 180 views
ADD COMMENTlink modified 11 months ago by ATpoint38k • written 11 months ago by pyKey50
0
gravatar for ATpoint
11 months ago by
ATpoint38k
Germany
ATpoint38k wrote:

Use option -bg to generate a bedGraph and then transform to bigwig using bedGraphToBigWig which can be read into IGV. Alternatively use bamCoverage from deeptools which essentially does the same but in one command.

ADD COMMENTlink written 11 months ago by ATpoint38k
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