extracting strand information from BAM to BED

Question

[amitpande74]

Hi everyone,

I have used bedtools bamtobed to extract information. My file looks like this:

chr10   1195932 1195977 NB551726:5:H2HT5BGXC:1:11101:11237:5492 41  + 
chr10   1195932 1195977 NB551726:5:H2HT5BGXC:1:11101:22230:17587    41  +

I am loosing the strand information when I tried bedtools merge command to remove the repeated coordinates. chr10 1195932 1195979

What I would want is an output like this :

chr10   1195932 1195977 NB551726:5:H2HT5BGXC:1:11101:11237:5492 41  +

for all the duplicated regions in one chromosome.

Can someone help.

Regards

[jean.elbers]

I can't guarantee that this will work in all cases, but maybe try bedtools merge -i test.bed -c 4,5,6 -o distinct|perl -pe 's/,\S+//g'. It assumes the file in your example is called test.bed.

Answer 1

[ATpoint]

A workaround could be to use the stranded option (-s) together with -o and -c:

cat test.bed 
chr10   1195932 1195977 NB551726:5:H2HT5BGXC:1:11101:11237:5492 41  +
chr10   1195932 1195977 NB551726:5:H2HT5BGXC:1:11101:22230:17587    41  +
chr10   1195932 1195977 NB551726:5:H2HT5BGXC:1:11101:11237:5492 41  -
chr10   1195932 1195977 NB551726:5:H2HT5BGXC:1:11101:22230:17587    41  -

bedtools merge -s -i test.bed -c 6 -o first
chr10   1195932 1195977 +
chr10   1195932 1195977 -

Essentially, it merges strand-specifically and then prints the first value (-o first) of the 6th columns (-c 6). Could be customized to include the first element of $5 and $6 pretty much as jean.elbers suggests above, but without summoning the Perl devil :-D

Also possible, simply merge without respect to strand and simply appending all the infos in $4, $5, and $6:

bedtools merge -i test.bed -c 4,5,6 -o collapse -delim "|"
chr10   1195932 1195977 NB551726:5:H2HT5BGXC:1:11101:11237:5492|NB551726:5:H2HT5BGXC:1:11101:22230:17587|NB551726:5:H2HT5BGXC:1:11101:11237:5492|NB551726:5:H2HT5BGXC:1:11101:22230:17587   41|41|41|41 +|+|-|-