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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
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groupBy won't group #41

Closed bchen4 closed 7 years ago

bchen4 commented 7 years ago

Hi, I am using Bedtools 2.26 groupBy function and I have a demo.bed.

chr1  3803892 3803908 BRN_IP_WT_A_pos_1 14  +
chr1  3803892 3803908 BRN_IP_A_S2_positive_1  14  +
chr1  4493610 4493620 BRN_IP_WT_A_pos_2 3 +
chr1  4493610 4493620 BRN_IP_A_S2_positive_2  3 +
chr1  4529016 4529066 BRN_IP_WT_A_pos_3 7 +
chr1  4529016 4529066 BRN_IP_A_S2_positive_3  7 +
chr1  4529070 4529123 BRN_IP_WT_A_pos_4 29  +
chr1  4529070 4529123 BRN_IP_A_S2_positive_4  29  +
chr1  4815570 4815584 BRN_IP_WT_A_pos_5 3 +
chr1  4815570 4815584 BRN_IP_A_S2_positive_5  3 +
chr1  4845221 4845223 BRN_IP_WT_A_pos_6 3 +
chr1  4845221 4845223 BRN_IP_A_S2_positive_6  3 +

And the commend and output I got was:

groupBy -i demo.bed -c 5 -g 1,2,3 -o sum
148

Basically, it did not really group my bed records, and the output is a single number which sum up all the scores of all records.

I also changed g and o but I got the similar no-groupby results.

From the help I think I was doing the correct thing.

    $ cat ex1.out
    chr1 10  20  A   chr1    15  25  B.1 1000    ATAT
    chr1 10  20  A   chr1    25  35  B.2 10000   CGCG

    $ groupBy -i ex1.out -g 1,2,3,4 -c 9 -o sum
    chr1 10  20  A   11000

I should expect the columns I used to do the grouping (specified by -g) should be printed out, correct? I am confused why this happened and by search Google I did not find any case like this.

I appreciate your help.

tjakobi commented 7 years ago

Hi @bchen4,

from your report it seems you are reporting a bedtools problem and not a problem related to the DCC software?

The Issue tracking system from bedtools may be found here: https://github.com/arq5x/bedtools2/pulls

Cheers, Tobias

bchen4 commented 7 years ago

Ops.... I clicked Google link. Sorry I did not look twice... Please delete this issue....