deeptools/3.3.1

[Mehrnush Forutan]

Hi all,

I am using deeptools/3.3.1 with a command " bamCoverage -b alignment.bam -o out.fwd.bw --samFlagExclude 16 --minMappingQuality 20 --exactScaling --binSize 1 -p 6" to generate coverage output per each position, but the output is different from my expectation!

For example, the current output is:

           seqnames        ranges            strand |     score

              <Rle>          <IRanges>      <Rle>  | <numeric>

        [1] NC_037328.1        16285           *     |         *

        [2] NC_037328.1   16286-16309     *     |         *

        [3] NC_037328.1        16310           *     |         *

        [4] NC_037328.1        16311           *     |         *

        [5] NC_037328.1   16312-16338     *     |        *

while I expected to be as:

  seqnames        ranges            strand |     score

              <Rle>          <IRanges>      <Rle>  | <numeric>

        [1] NC_037328.1        16285           *     |         *

        [2] NC_037328.1        16286           *     |         *

        [3] NC_037328.1        16287           *     |         *

        [4] NC_037328.1        16288           *     |         *

        [5] NC_037328.1        16289           *     |         *

would you please let me know what command should I use to get the coverage only for each bp not the ranges?

Thanks in advance,

Mehrnush

----------------​
Mehrnush Forutan

Postdoctoral Research Fellow | Centre for Animal Science

Queensland Alliance for Agriculture and Food Innovation

The University of Queensland

Brisbane Qld 4072 Australia

 M +61435733389

E mehrnush...@gmail.com,  m.fo...@uq.edu.au

[Devon Ryan]

DeepTools merges bases that have the same coverage since the output is
then smaller but otherwise identical.
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany

> --
> You received this message because you are subscribed to the Google Groups "deepTools" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to deeptools+...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/deeptools/ME2PR01MB50128CC3273B9B6001CD3C2FA83F0%40ME2PR01MB5012.ausprd01.prod.outlook.com.