Merge Bed files but keep optional columns

Question

[melissa.ilsley]

I have 2 Bed files that i need to merge. I have done so using the following command and it has worked fine.

 bedtools merge -c 1 -o count -i ~/Temp_output/peak_count_analysis/Klf3/MACS2/Klf3_ChIP_summits200.bed -i ~/Temp_output/peak_count_analysis/Klf1/MACS2/Klf1_K1ER_pool_summits200.bed > ~/Temp_output/peak_count_analysis/merged/mergedsummits200.bed 

However, this results in lost of a lot of useful information for downstream analysis.

Is there a way to merge files and keep the information for those regions? If so, can the merged regions just combine the information into the one column?

Example:

File 1:

chr1   5251857 5252058 Klf1_K1ER_pool_peak_1   13.22945

chr1    9770501 9770702 Klf1_K1ER_pool_peak_2   6.61350

chr1    9773611 9773812 Klf1_K1ER_pool_peak_3   2.72345

chr1    9774350 9774551 Klf1_K1ER_pool_peak_4   40.70829

chr1    9815269 9815470 Klf1_K1ER_pool_peak_5   22.47497

...

File 2:

chr1   6204622 6204823 Klf3_ChIP_peak_1    0.88333

chr1    7078830 7079031 Klf3_ChIP_peak_2    19.91139

chr1    7388243 7388444 Klf3_ChIP_peak_3    15.39874

chr1    9690724 9690925 Klf3_ChIP_peak_4    7.17301

chr1    9738376 9738577 Klf3_ChIP_peak_5    8.30267

...

Hopeful outcome:

chr1   6204622 6204823 2   Klf3_ChIP_peak_1; Klf1_K1ER_pool_peak_5

chr1    9770501 9770702 1   Klf1_K1ER_pool_peak_2

...

I need to eventually convert the merged file to a gtf and would like to retain peak information.

Thanks in advance.

Answer 1

[dariober]

Just give to mergeBed more columns to group via the -c and -o options. For example:

cat file1.bed 
chr1    5251857 5252058 Klf1_K1ER_pool_peak_1   13.22945
chr1    9770501 9770702 Klf1_K1ER_pool_peak_2   6.61350
chr1    9773611 9773812 Klf1_K1ER_pool_peak_3   2.72345
chr1    9774350 9774551 Klf1_K1ER_pool_peak_4   40.70829
chr1    9815269 9815470 Klf1_K1ER_pool_peak_5   22.47497

cat file2.bed 
chr1    5251857 5252058 Klf1_K1ER_pool_peak_6   13.22945
chr1    9770501 9770702 Klf1_K1ER_pool_peak_7   6.61350
chr1    9773611 9773812 Klf1_K1ER_pool_peak_8   2.72345
chr1    9774350 9774551 Klf1_K1ER_pool_peak_9   40.70829
chr1    9815269 9815470 Klf1_K1ER_pool_peak_10  22.47497

Retain information on column 4 and 5:

sort -k1,1 -k2,2n file1.bed file2.bed \
| mergeBed -c 4,4,5 -o count,collapse,collapse
chr1    5251857 5252058 2   Klf1_K1ER_pool_peak_1,Klf1_K1ER_pool_peak_6 13.22945,13.22945
chr1    9770501 9770702 2   Klf1_K1ER_pool_peak_2,Klf1_K1ER_pool_peak_7 6.61350,6.61350
chr1    9773611 9773812 2   Klf1_K1ER_pool_peak_3,Klf1_K1ER_pool_peak_8 2.72345,2.72345
chr1    9774350 9774551 2   Klf1_K1ER_pool_peak_4,Klf1_K1ER_pool_peak_9 40.70829,40.70829
chr1    9815269 9815470 2   Klf1_K1ER_pool_peak_10,Klf1_K1ER_pool_peak_5    22.47497,22.47497

[melissa.ilsley]

Ah. that's what i thought i might need to do, but wasn't sure how to do it. thank you.

[melissa.ilsley]

ok. i see what you are doing there.

[melissa.ilsley]

Hi again,

For some reason, when i sort it with the options you give (specifically the -k2,2n) bedtools merge cannot open the file.

I don't understand this.

to actually get it sorted in the correct order I need the options: -k1,1V -k2,2n (your options sorte Chr 1, Chr 10, Chr 11..). If i do it with just -k1,V1, bedtools and open it but it's not sorted by start properly, but it can at least open it.

annoyingly, once i get it sorted properly, it won't open it but i can't tell what is wrong with it to fix it!

any help is greatly appreciated.