bedtools error

[cmccabe]

I am getting the below error using bedtoold 2.20. The files are too large to attach. Thank you.

 dnascopev@ubuntu:~$ cd "/media/9C168A3F168A1A82"

dnascopev@ubuntu:/media/9C168A3F168A1A82$ coverageBed -hist -abam IonXpress_001.bam -b LCH_IDT.bed | grep ^all > output.txt
Unexpected file format.  Please use tab-delimited BED, GFF, or VCF. Perhaps you have non-integer starts or ends at line 1?

[dpryan]

What're the first couple lines of LCH_IDT.bed?

[cmccabe]

There are 15 lines in that file sorted: The first 3 lines are below. Thanks.

chr12 112884064 112884217
chr12 112888106 112888331
chr12 112890983 112891206

[dpryan]

The most common cause of this is either not using unix line endings (i.e., using \r) or having an extraneous space after a tab. The simplest thing is to just look at the bed file in a hex editor. You could also just "od -c LCH_IDT.bed" if you don't have a hex editor handy. A tab will show up as "\t" and a proper like ending will be "\n". Aside from those you should only see regular characters.

[cmccabe]

Thank you, that was it... I seem to do that a lot, I guess I need to use Linux more and Windows less .

[dariober]

For the record... To quickly visualize non-printable characters you could use

cat -vet

. What you want to see is that tab characters are marked by ^I and line endings by $. If lines end in ^M$ you have windows line endings "carriage return + line feed". E.g.:

cat -vet ds069_293T_GFP_2.merge_peaks.bed | head
chr1^I713939^I714220^Ids069_293T_GFP_2.merge_peak_1^I8.91011$
chr1^I762786^I762945^Ids069_293T_GFP_2.merge_peak_2^I6.57885$
chr1^I805256^I805387^Ids069_293T_GFP_2.merge_peak_3^I3.11743$
chr1^I840046^I840238^Ids069_293T_GFP_2.merge_peak_4^I3.39438$
chr1^I856585^I856713^Ids069_293T_GFP_2.merge_peak_5^I7.55995$
chr1^I859179^I859369^Ids069_293T_GFP_2.merge_peak_6^I13.05689$

[cmccabe]

Thank you .