bedtools multiple BAM files

Question

[amitpande74]

I have BAM files in the external hard drive. Want to convert them into BED. Am using

cd /media/usr/LaCie/work/client/pool1/bam
for x in *.bam ; do
    echo "print current:$x";
    bedtools bamToBed -i "$x" > "${x%.bam}.bed";
done
echo "done"

it writes the BED files in the directory, but they are all empty. My BEDtools is installed in

/home/usr/miniconda3/bin/bedtools

Can someone tell me where I am going wrong? And the BAM files have reads, so there is no problem there. regards.

[Pierre Lindenbaum]

any error message on your screen ?

[amitpande74]

error: unrecognized command: bamToBed

[husensofteng]

change bamToBed to bamtobed (small letters).

[Pierre Lindenbaum]

Hello amitpande74!

It appears that your post has been cross-posted to another site: https://stackoverflow.com/questions/64860327

This is typically not recommended as it runs the risk of annoying people in both communities.

[amitpande74]

(base) samtools view A1_S1.bam | head
NS500455:81:HTVKJBGXC:1:12305:10402:19515   16  chr1    231634  1   43M *   0   0   AGAATTGGGTTGGAATTTTGATGGGGATTGCATTGAATCTGTA <EE<A<EAEAEAA/EEAEEEEAAAAEEEEE/EEAAEEEA/EEE AS:i:86 XS:i:86 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:43 YT:Z:UU
NS500455:81:HTVKJBGXC:2:22109:7726:14155    16  chr1    231634  1   43M *   0   0   AGAATTGGGTTGGAATTTTGATGGGGATTGCATTGAATCTGTA EEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE AS:i:86 XS:i:86 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:43 YT:Z:UU
NS500455:81:HTVKJBGXC:3:22505:6042:9122 16  chr1    231634  1   43M *   0   0   AGAATTGGGTTGGAATTTTGATGGGGATTGCATTGAATCTGTA EE<E/<EAEEAEEEEAEA/EA<AEEEE<AEEE<<AAEAEEAEE AS:i:86 XS:i:86 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:43 YT:Z:UU
NS500455:81:HTVKJBGXC:1:12101:2573:8192 0   chr1    312297  1   37M6S   *   0   0   TATATAATAAATGAATAAATCTTTAAAAAAAAAAAAGGCCTGA EEEEEAEA<EEEEEEEEEEEEEAEEEE<E<EAEEEAAEEAAAE AS:i:74 XS:i:74 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:37 YT:Z:UU
NS500455:81:HTVKJBGXC:1:21211:14672:4155    0   chr1    312297  1   37M6S   *   0   0   TATATAATAAATGAATAAATCTTTAAAAAAAAAAAAGGCCTGA EEEEEEEEAAEEEEAEAEEEEEAEAAEEEEEEAEEAE/EAA<E AS:i:74 XS:i:74 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:37 YT:Z:UU
NS500455:81:HTVKJBGXC:2:21107:10835:2883    0   chr1    312297  11  37M6S   *   0   0   TATATAATAAATGAATAAATCTTTAAAAAAAAAAAAGGCCTGA EEEEE6/E6A/AEA/EAAEEAEEE///<AAEEAEEEEEAEEA< AS:i:74 XS:i:73 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:37 YT:Z:UU
NS500455:81:HTVKJBGXC:4:12504:22831:18864   0   chr1    312297  1   37M6S   *   0   0   TATATAATAAATGAATAAATCTTTAAAAAAAAAAAAGGACCTC EEEE/E/////E//<E<6A//E/AEEA6E/E/A////////// AS:i:74 XS:i:74 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:37 YT:Z:UU
NS500455:81:HTVKJBGXC:3:21402:6383:13492    16  chr1    348070  1   44M *   0   0   AATTTGCAAATTCATCTGGAATAACAAAAAAACCAGGATAGCTA    EEAE<EEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAEE    AS:i:88 XS:i:88 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:44 YT:Z:UU
NS500455:81:HTVKJBGXC:1:22102:3644:3920 16  chr1    348071  1   43M *   0   0   ATTTGCAAATTCATCTGGAATAACAAAAAAACCAGGATAGCTA EEEEEEEEEAAEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEE AS:i:86 XS:i:86 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:43 YT:Z:UU
NS500455:81:HTVKJBGXC:1:22303:6790:10657    16  chr1    348071  1   43M *   0   0   ATTTGCAAATTCATCTGGAATAACAAAAAAACCAGGATAGCTA EEAEEEAEEAAEA<AEE

[Pierre Lindenbaum]

after I added a fake header to your sam, it worked fine on my machine.

$ for x in ~/jeter.bam; do echo "current $x"; bedtools bamtobed -i "${x}" > "${x%.bam}.bed" ; done && cat ~/jeter.bed
current /path/to/jeter.bam
chr1    231633  231676  NS500455:81:HTVKJBGXC:1:12305:10402:19515   1   -
chr1    231633  231676  NS500455:81:HTVKJBGXC:2:22109:7726:14155    1   -
chr1    231633  231676  NS500455:81:HTVKJBGXC:3:22505:6042:9122 1   -
chr1    312296  312333  NS500455:81:HTVKJBGXC:1:12101:2573:8192 1   +
chr1    312296  312333  NS500455:81:HTVKJBGXC:1:21211:14672:4155    1   +
chr1    312296  312333  NS500455:81:HTVKJBGXC:2:21107:10835:2883    11  +
chr1    312296  312333  NS500455:81:HTVKJBGXC:4:12504:22831:18864   1   +
chr1    348069  348113  NS500455:81:HTVKJBGXC:3:21402:6383:13492    1   -
chr1    348070  348113  NS500455:81:HTVKJBGXC:1:22102:3644:3920 1   -

[GenoMax]

Is there a header? What does

samtools view -H A1_S1.bam | head

show?

[Pierre Lindenbaum]

OP would have told us that there is an error message ...

[amitpande74]

Thanks @Pierre. I changed the cable of my external hard drive and now it works. Thanks to all for the kind support.

Answer 1

[Pierre Lindenbaum]

error: unrecognized command: bamToBed

bedtools bamtobed ....

[amitpande74]

I did correct it, yet it does not work.

[Friederike]

has the error message changed?

[amitpande74]

Now there is no error message...giving an impression that it works. But still cannot see it in the top command.It has made an empty file in the folder titled .bed....am waiting to see if the script writes anything there. Shall keep you all updated. Thanks for the patience you people have shown.

[Pierre Lindenbaum]

show us a few reads from a bam please.