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failing to convert gtf to bed by bedops

Hi,

I am using fedora. I have a merged.gtf by cuffdif that I am going to convert to bed because I need something like below (the first row of a bed file) that I have after mapping with bowtie2 and downstream tool to bed

YAL001C    0    31    SRR1944914.13670510    42    +

but here I used tophat and cufflinks and now I have a gtf that is the first row of my gtf file

1    Cufflinks    exon    3631    3913    .    +    .    gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "NAC001"; oId "AT1G01010.1"; nearest_ref "AT1G01010.1"; class_code "="; tss_id

I used this command to convert to bed format but I got error

[izadi@lbox161 bin]$ gtf2bed < merged.gtf | sort-bed - > file.bed
Segmentation fault
[izadi@lbox161 bin]$

Thank you for your help

bedops gtf bed
• 7,557 views • link
updated by Ram Ram • written by zizigolu zizigolu

First, why do you need sort-bed if gtf2bed already sorts the output?

Tip: By default, all conversion scripts now output sorted BED data ready for use with BEDOPS utilities. If you do not want to sort converted output, use the --do-not-sort option. Run the script with the --help option for more details.

Second, if you get an error, break apart your multiple commands and find out which one is giving you the error.

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written by h.mon h.mon

but i used only one command then how i can break that apart?

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written by zizigolu zizigolu

see |.

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written by h.mon h.mon

Fereshteh, as noted in my comment, the pre-compiled binaries may not work on all Linux systems. You can compile and install by hand with a few commands - instructions are posted here.

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updated by Ram Ram • written by Alex Reynolds Alex Reynolds

2 answers

I think the issue might be in the way you are piping things. This appeared to have worked for me:

cat merged.gtf | gtf2bed - | sort-bed - > file.bed

Though the GTF used in my test was not the output of cufflinks.

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updated by Ram Ram • written by A. Domingues A. Domingues

thank you,

but

[izadi@lbox161 bin]$ cat merged.gtf | gtf2bed | sort-bed - > file.bed
Segmentation fault
[izadi@lbox161 bin]$

and when I just use 

cat merged.gtf | gtf2bed > file.bed

nor error nor readable output

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updated by Ram Ram • written by zizigolu zizigolu

For some reasons unknown to me, Bedtools/Bedops never liked the output of gtf2bed with a Cufflinks style input. More precisely, the 6 first columns (up to the strand column) are ok but not the rest (with fields separated by ";"). Just use:

cat merged.gtf | gtf2bed  | cut -f-6 | someCommand

gtf2bed will use the gene_id field as the output bed 4th column (unique identifiers for each interval).

You can then use commands like awk and join if you need to merge the rest of your information. It is a dirty workaround, but it works.

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updated by Ram Ram • written by cyril-cros cyril-cros

sorry,

I did like below but the output is unreadable

cat merged.gtf | gtf2bed | cut -f-6 > file1.bed
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updated by Ram Ram • written by zizigolu zizigolu

I tried one of my own cufflinks file. You are right. Gtf2bed and convert2bed no longer seem to work. I had a really detailed and tested workflow which now fails at this step. I am currently looking if some recent change introduced a bug.

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written by cyril-cros cyril-cros

anyway thank you

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updated by Ram Ram • written by zizigolu zizigolu

I would be interested in fixing any problems with this tool. If you can post part of your file somewhere, and describe the platform you are running this on and what error comes up, that would help me do some debugging on my end.

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updated by Ram Ram • written by Alex Reynolds Alex Reynolds

Input (Cufflinks, from the sup. material of a paper on olfactory receptors):

1    reconstructed_transcript    exon    92571567    92571659    .    +    .    gene_id "CUFFORG_0001"; transcript_id "CUFFORT_0001"; exon_number "1"; gene_name "Olfr1413";
1    reconstructed_transcript    exon    92573464    92574374    .    +    .    gene_id "CUFFORG_0001"; transcript_id "CUFFORT_0001"; exon_number "2"; gene_name "Olfr1413"; ensembl_id "ENSMUSG00000058904";
1    ENSEMBL_transcript    exon    92573125    92574206    .    +    .    gene_id "CUFFORG_0001"; transcript_id "ENSMUST00000074859"; exon_number "1"; gene_name "Olfr1413"; ensembl_id "ENSMUSG00000058904";

I am using Archlinux, PKGBUILD is https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=bedops. That is, it downloads the 2.14.4 Github version of Bedops, uses sed to replace all explicit mention of /usr/bin/env python by /usr/bin/env python2 and installs the binaries in /usr/bin.

Running gtf2bed or convert2bed fails silently (no output or message, but I do get the usage display with a bad command).

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updated by Ram Ram • written by cyril-cros cyril-cros

Thanks. Do you have a link to the paper or doi? I can grab the file from the supplementary material in there.

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written by Alex Reynolds Alex Reynolds

Unfortunately, I'm not able to reproduce this bug with the given file under OS X 10.11 running BEDOPS 2.4.14 tools. I get a complete BED output, with all the same records. I'll see if I can set up an Archlinux VM at work sometime in the next few days to try to reproduce it there.

In the meantime, instead of using that third-party PKGBUILD script, you (and others) could also compile the toolkit manually, which isn't too hard to do. The pre-compiled binaries may require a newer kernel than what is on the variety of Linux systems out there, and compiling by hand addresses that issue.

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updated by Ram Ram • written by Alex Reynolds Alex Reynolds

sorry,

I did like you mentioned but

/bin/ld: cannot find -lstdc++
collect2: error: ld returned 1 exit status
Makefile:40: recipe for target 'build' failed
make[3]: *** [build] Error 1
make[3]: Leaving directory '/usr/data/nfs6/izadi/bedtools2/bin/bedops/applications/bed/bedmap/src'
/usr/data/nfs6/izadi/bedtools2/bin/bedops/system.mk/Makefile.linux:29: recipe for target 'applications/bed/bedmap/src' failed
make[2]: *** [applications/bed/bedmap/src] Error 2
make[2]: Leaving directory '/usr/data/nfs6/izadi/bedtools2/bin/bedops'
system.mk/Makefile.linux:20: recipe for target 'default' failed
make[1]: *** [default] Error 2
make[1]: Leaving directory '/usr/data/nfs6/izadi/bedtools2/bin/bedops'
Makefile:14: recipe for target 'default' failed
make: *** [default] Error 2
[izadi@lbox161 bedops]$
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updated by Ram Ram • written by zizigolu zizigolu

You may need to install a newer version of GCC tools. See the compile instructions for more details.

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updated by Ram Ram • written by Alex Reynolds Alex Reynolds

If you are running a RH-like Linux, you may also want to install static versions of common libraries:

$ sudo yum install libstdc++-static
$ sudo yum install glibc-static

This seems to fix some cases of cannot find -lXYZ error messages.

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updated by Ram Ram • written by Alex Reynolds Alex Reynolds

I don't know if it help with the debbuding, but I download the paper's GTF and 

cat journal.pgen.1004593.s017.GTF | gtf2bed | sort-bed - | head

runs without a itch.

bedops version:

gtf2bed --version
convert2bed -i gtf
  version: 2.4.12
  author:  Alex Reynolds

System:

Linux 3.16.0-0.bpo.4-amd64 #1 SMP Debian 3.16.7-ckt11-1~bpo70+1 (2015-06-08) x86_64
• 0 views • link
updated by Ram Ram • written by A. Domingues A. Domingues

I installed the current version of Archlinux:

# uname -a
Linux archlinux-retina 4.2.5-1-ARCH #1 SMP PREEMPT Tue Oct 27 08:13:28 CET 2015 x86_64 GNU/Linux

After installing git and downloading BEDOPS source, I compiled it with the GCC 5.2.0 distribution that is packaged with the base-devel package in Archlinux.

I then converted the PLoS GTF file to BED via gtf2bed without any errors. I get the same number of records and data are in the correct columnar order.

If you have problems, my advice would be to download the source and recompile/reinstall binaries via the instructions on the BEDOPS docs site.

• 0 views • link
updated by Ram Ram • written by Alex Reynolds Alex Reynolds

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