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bedmap / Re: No tabs found in BED row.
« Last post by AlexReynolds on October 20, 2017, 11:12:54 AM »

Can you please replace sort -k1,1 with sort-bed -? (Please include the hyphen.) I'm not sure why you get that error, but it does look like your data might not be sorted correctly, and so that is something you'd want to change, in any case.

You can use cat -te to check for both tab and newline characters. If your BED files come from Excel or Windows, there could be additional carriage-return characters in there that would cause problems with parsing.

If you can share the files BAM/Big_Data_ref.fa.bed and Big_Data_ref_mappability.wig.bed, that would be helpful, as well as what version of the toolkit you are using, and on what platform you're running things.
bedmap / No tabs found in BED row.
« Last post by claudius on October 20, 2017, 10:50:28 AM »

when I run the following command:

Code: [Select]
bedmap --ec --mean <(awk 'BEGIN{OFS="\t"}{$3-=40; print}' BAM/Big_Data_ref.fa.bed | sort -k1,1) Big_Data_ref_mappability.wig.bed > Big_Data_ref_mappability.mean.bed

... I get the following error message:

Error: in /dev/fd/63
No tabs found in BED row.
See row: 1

However, running:

Code: [Select]
awk 'BEGIN{OFS="\t"}{$3-=40; print}' BAM/Big_Data_ref.fa.bed | sort -k1,1 | head | cat -t


So my reference bed file should be tab delimited.

What's going wrong here?

bedops / Re: Bedops closest-feature header issue
« Last post by sjn on June 06, 2017, 09:35:43 AM »
Thanks for joining the forum.

The tab delimited columns are your inputs.

The default output delimiter is '|'.  You have 3 columns, the reference element is the first one, which has 12 tab-delimited columns or so.  The second column is the closest element, which has 5 tab-delimited columns or so, and then the 3rd column is the distance.

You can suppress the first column (reference element) using the --no-ref option.  If you are solely looking for the distances and do not care about the actual element information, then you can use the `cut` command:
closest-features --dist --closest 100_bedops_sorted.bed DBsites060517_bedops_sorted.bed | cut -f3 -d'|' > test.out

or, if you include --no-ref:
closest-features -no-ref --dist --closest 100_bedops_sorted.bed DBsites060517_bedops_sorted.bed | cut -f2 -d'|' > test.out

If you are interested in the closest element, then no `cut` is needed.

You can change the output delimiter using the --delim option.
bedops / Bedops closest-feature header issue
« Last post by rbronste on June 06, 2017, 08:45:56 AM »

In getting the output for this, since it doesn't print a header having a hard time discerning all of the different output columns are in the BED file, is there a way to print a header for this? Just looking to see distance from closest features, and those are options I have invoked. Including an example of the output and command below. Thanks.


closest-features --dist --closest 100_bedops_sorted.bed DBsites060517_bedops_sorted.bed > test.bed
bedops / Re: Multi threading in bedops
« Last post by sjn on May 11, 2017, 09:14:38 AM »
The most effective way to use BEDOPS is to process data by chromosome.  Each utility takes a chromosome name as an option.  For example:

bedops -e --chrom chr18 file1.bed file2.bed file3.bed file4.bed

This will do work only on chr18.  So, looping through every chromosome and running each in parallel is often very effective.  This can be done cluster-wide, or as background processes on a multiprocessor machine.  Then, you can quickly glue the results back together with a simple call to cat (or starchcat if outputs are in Starch format).

True multi-threading (not multi-processing) is not very effective for most utilities as outputs maintain sorted order.  Even if you can calculate items in parallel, it must all be synchronized at the output.  We are experimenting with where multithreading can be used effectively, however.

If you have a specific example of what you are trying to achieve, we often have ways to show how to speed things up.  For example, bedextract can be much faster than bedops -e when its data preconditions are met.  Also, bedmap --faster can be a huge help in cases where it applies, as can piping commands efficiently, sometimes using named pipes.  We do take great care in keeping our tools general and fast, so we are definitely interested in cases where the tools are not performing at speeds that you find acceptable.  Please send details.

We are also looking to have some pretty big speedups in our next release of BEDOPS for several utilities.
bedops / Multi threading in bedops
« Last post by chudar on April 22, 2017, 12:03:57 AM »

I am using bedops for my analysis. I would like to know how can i make use of multi threads in bedops to speed up the process. Kindly guide me
Conversion tools to BED format / Re: Error in gtf2bed
« Last post by AlexReynolds on February 15, 2017, 10:01:01 PM »
Thanks! I'm away for a couple weeks, but I will investigate when I get back. I have a ticket here where you can follow any future commits/patches to this issue:
Conversion tools to BED format / Re: Error in gtf2bed
« Last post by zebasilio on February 15, 2017, 03:26:56 AM »
Dear Alex,

The gtf file is from a igenome mouse annotation : .The remaining requested info are in the attached files

Thank you,
Conversion tools to BED format / Re: Error in gtf2bed
« Last post by AlexReynolds on February 14, 2017, 01:27:24 AM »
Can you please send me a copy of your GTF file? (If you can post it publicly.) Also, can you please describe your host environment? Thanks!
Conversion tools to BED format / Error in gtf2bed
« Last post by zebasilio on February 14, 2017, 12:44:39 AM »

I am trying to convert a gtf to a bed file but I am always getting this error message:

$gtf2bed < genes.gtf > genes.gtf.bed

*** Error in `convert2bed': realloc(): invalid next size: 0x0000000001337f60 ***
/home/jose/bin/gtf2bed: line 122: 16784 Aborted                 (core dumped) ${cmd} ${options} - 0<&0

I am using version:  2.4.24

Thanks for your help. Josť
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