Error with bedtools intersect

Question

[galeandrewn]

I am trying to run bedtools intersect on some sequencing data for acetylation and methylation compared to the UGSC genome database to extract genes that are acetylated and methylated or just have one. When I try to run the intersect function i receive this error

Error: Unable to open file NewMacsSortedMappedMethylAndControlSRR500128_peaks.narrowPeak,. Exiting.

These are the first few lines of each file. I am extremely new to this all so that may be part of my problem.

UGSC genome

chr19   3066555 3066627 uc033hid.1  0   +   3066555 3066555 0   1   72, 0,
chr19   3153210 3197703 uc008fvy.2  0   -   3153210 3153210 0   4   191,79,85,99,   0,720,43734,44394,
chr19   3153798 3197703 uc008fvz.2  0   -   3153798 3153798 0   3   211,85,99,  0,43146,43806,

First file

chr19   3001043 3001162 MacsSortedMappedAcetylAndControlSRR500128_peak_1    97  .   4.55619 13.63534    9.79101 32
chr19   3002259 3002379 MacsSortedMappedAcetylAndControlSRR500128_peak_2    24  .   2.68011 4.82869 2.49843 86
chr19   3003784 3003959 MacsSortedMappedAcetylAndControlSRR500128_peak_3    157 .   9.13436 20.45238    15.71352    81
chr19   3004910 3005073 MacsSortedMappedAcetylAndControlSRR500128_peak_4    35  .   2.79306 6.14924 3.55281 108
chr19   3007329 3007483 MacsSortedMappedAcetylAndControlSRR500128_peak_5    32  .   3.20514 5.73549 3.21243 59
chr19   3010655 3010845 MacsSortedMappedAcetylAndControlSRR500128_peak_6    78  .   3.93533 11.38407    7.86583 102

second file

chr19   3001045 3001156 MacsSortedMappedMethylAndControlSRR500128_peak_1    45  .   3.13242 7.53378 4.58204 17
chr19   3002255 3002430 MacsSortedMappedMethylAndControlSRR500128_peak_2    50  .   3.42686 8.13604 5.08095 92
chr19   3034512 3034724 MacsSortedMappedMethylAndControlSRR500128_peak_3    95  .   3.90128 13.36253    9.59686 121
chr19   3035532 3035718 MacsSortedMappedMethylAndControlSRR500128_peak_4    71  .   2.93796 10.56525    7.15992 94
chr19   3036486 3036609 MacsSortedMappedMethylAndControlSRR500128_peak_5    104 .   3.62301 14.30489    10.42895    65

Both files are sorted by macs and are the peaks.narrowpeaks output. Once again I am fairly new so I apologize if this is a rookie question.

[GouthamAtla]

What's the output of

head -3 file1 file2

Though you have posted the first lines, I would like to make sure the files are accessible.

[A. Domingues]

What does this line:

UGSC genome chr19 3066555 3066627 uc033hid.1 0 + 3066555 3066555 0 1 72, 0, chr19 3153210 3197703 uc008fvy.2 0 - 3153210 3153210 0 4 191,79,85,99, 0,720,43734,44394, chr19 3153798 3197703 uc008fvz.2 0 - 3153798 3153798 0 3 211,85,99, 0,43146,43806,

Represent? If that is part of one the files beingintersected it could be the reason bedtools is breaking. It is not a properly formated bed file. The other lines also look a bit iffy.

[michael.ante]

Could you please post the commands you used for the intersect call?

Answer 1

[Sukhi Singh]

The files are fine, your input command has a problem. The tool is not able to locate the file (I reckon a typo).

[A. Domingues]

The files are fine,

yep. I commented before post was nicely formated by you :)

[Sukhi Singh]

No worries, some new users (new to Q/A and forums) are not aware of the formatting tools, which changes the whole perspective.