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Forum: Bioinformatics 03-25-2015, 01:13 PM
Replies: 7
Views: 1,244
Posted By AlexReynolds
You can use BEDOPS...

You can use BEDOPS (http://bedops.readthedocs.org/en/latest/) bam2bed to convert from BAM to BED, pipe to bedops to merge overlapping elements, and pipe to bedmap to generate a list of lengths per...
Forum: RNA Sequencing 03-25-2015, 11:22 AM
Replies: 6
Views: 1,531
Posted By AlexReynolds
As noted in another question, convenience wrapper...

As noted in another question, convenience wrapper scripts are provided to convert SAM and other formats to BED and Starch (compressed BED):

$ sam2bed < 1.sam > 1.bed
$ sam2starch < 1.sam >...
Forum: Bioinformatics 03-25-2015, 11:20 AM
Replies: 3
Views: 941
Posted By AlexReynolds
BEDOPS offers bedmap, for mapping features from...

BEDOPS offers bedmap, for mapping features from one BED file to another. It is fast and efficient, and supported on Linux. Operations are offered that work with numerical and categorical features.
...
Forum: RNA Sequencing 03-25-2015, 11:15 AM
Replies: 4
Views: 2,443
Posted By AlexReynolds
I also include convenience wrapper scripts with...

I also include convenience wrapper scripts with BEDOPS, so that you can do:

$ sam2bed < 1.sam > 1.bed
$ sam2starch < 1.sam > 1.starch

Similar wrapper scripts are available for other formats...
Forum: Bioinformatics 02-19-2015, 12:18 AM
Replies: 2
Views: 2,181
Posted By AlexReynolds
You could probably modify this script for your...

You could probably modify this script for your input sets:

​#!/usr/bin/env python

input_one = '''
BIEC2-99962 HOR_233 G_G
BIEC2-9997 HOR_233 A_G
BIEC2-999748 HOR_233 C_C
BIEC2-999848...
Forum: Bioinformatics 01-23-2015, 01:30 PM
Replies: 7
Views: 2,260
Posted By AlexReynolds
That error usually means that the process ran out...

That error usually means that the process ran out of usable memory. This can be due to either the program trying to allocate more space than is available, or there is a memory leak that is exposed...
Forum: Bioinformatics 01-02-2015, 10:32 AM
Replies: 0
Views: 1,072
Posted By AlexReynolds
BEDOPS 2.4.3 released

BEDOPS 2.4.3 release (GitHub) (https://github.com/bedops/bedops/releases/tag/v2.4.3)

Compilation improvements


Shane Neph put in a great deal of work to enable parallel builds (e.g., make -j...
Forum: Bioinformatics 07-01-2014, 09:09 AM
Replies: 3
Views: 1,840
Posted By AlexReynolds
You can use BEDOPS sort-bed to sort BED files: ...

You can use BEDOPS sort-bed to sort BED files:

http://bedops.readthedocs.org/en/latest/content/reference/file-management/sorting/sort-bed.html

GNU sort is not as fast as sort-bed (even with...
Forum: RNA Sequencing 10-02-2013, 08:07 AM
Replies: 12
Views: 3,895
Posted By AlexReynolds
We have posted new builds of BEDOPS v2.3: ...

We have posted new builds of BEDOPS v2.3:

https://github.com/bedops/bedops/releases/tag/v2.3.0

A more complete revision history is available here:
...
Forum: Bioinformatics 10-02-2013, 07:44 AM
Replies: 25
Views: 18,812
Posted By AlexReynolds
We have posted BEDOPS v2.3, which includes a...

We have posted BEDOPS v2.3, which includes a fixed gff2bed script:

https://github.com/bedops/bedops/releases/tag/v2.3.0

A more complete revision history is available here:
...
Forum: Bioinformatics 09-24-2013, 02:47 AM
Replies: 25
Views: 18,812
Posted By AlexReynolds
There has been a change to the GTF standard, such...

There has been a change to the GTF standard, such that gtf2bed fails to parse newer GTF files (such as the example input that you link to, thanks).

This conversion script will be fixed in BEDOPS...
Forum: Bioinformatics 08-27-2013, 09:53 AM
Replies: 25
Views: 18,812
Posted By AlexReynolds
That appears to be a different error from what is...

That appears to be a different error from what is described in a previous comment. Thanks for the error report and sample GFF file. I'll take a look when I can.
Forum: Bioinformatics 07-30-2013, 02:16 PM
Replies: 1
Views: 1,670
Posted By AlexReynolds
Perhaps you could try passing the output from the...

Perhaps you could try passing the output from the sam2bed script (http://code.google.com/p/bedops/wiki/sam2bed) to the bed2psl.py script...
Forum: RNA Sequencing 06-12-2013, 10:53 AM
Replies: 12
Views: 3,895
Posted By AlexReynolds
For others, I posted a new OS X installer...

For others, I posted a new OS X installer ("2.2.0b") that fixes this issue:

http://code.google.com/p/bedops/downloads/detail?name=bedops_macosx_intel_fat-v2.2.0b.mpkg.zip

This patches some...
Forum: RNA Sequencing 06-12-2013, 10:29 AM
Replies: 12
Views: 3,895
Posted By AlexReynolds
Thanks, the paths that otool are reporting are...

Thanks, the paths that otool are reporting are wrong. I'm researching why that is.

In the meantime, to resolve this issue please run the following commands:

$ sudo install_name_tool -change...
Forum: RNA Sequencing 06-12-2013, 09:20 AM
Replies: 12
Views: 3,895
Posted By AlexReynolds
That's the current version. Can you post the...

That's the current version. Can you post the results from the following command?

$ otool -L /usr/local/bin/bedmap

You may need to install otool via Xcode or Apple's command-line developer tools...
Forum: RNA Sequencing 06-12-2013, 08:27 AM
Replies: 12
Views: 3,895
Posted By AlexReynolds
Can you indicate what version of bedmap you are...

Can you indicate what version of bedmap you are running? This is an error usually seen with an older version of BEDOPS for OS X, and upgrading to a current version may help resolve this.
Forum: Bioinformatics 06-05-2013, 03:22 PM
Replies: 3
Views: 2,055
Posted By AlexReynolds
I think dgscofield is right — while BAM is...

I think dgscofield is right — while BAM is 0-based, the output from SAM is still 1-based. Easy to screw up. Subtracting one from the start coordinate in my awk script should fix the indexing.
Forum: Bioinformatics 06-05-2013, 04:53 AM
Replies: 3
Views: 2,055
Posted By AlexReynolds
Perhaps a basic awk script would work: $ awk...

Perhaps a basic awk script would work:

$ awk 'BEGIN{\
first_start=$2;\
old_start=first_start;\
}\
{\
chr=$1;\
current_start=$2;\
if (current_start > (old_start + 1)) {\
Forum: RNA Sequencing 06-05-2013, 04:39 AM
Replies: 12
Views: 3,895
Posted By AlexReynolds
If you can get your reads and your genes into...

If you can get your reads and your genes into UCSC BED format, then you can use the BEDOPS bedmap tool to map reads to genes.

http://code.google.com/p/bedops/wiki/bedmap

The bedmap tool comes...
Forum: Bioinformatics 06-03-2013, 02:48 PM
Replies: 6
Views: 2,096
Posted By AlexReynolds
If you're looking for promoters or TF binding...

If you're looking for promoters or TF binding sites that are proximal to your gene, where you define proximal as some sensible value (say, between 1000-2500 bases; this depends on your work) then...
Forum: Bioinformatics 06-03-2013, 02:41 PM
Replies: 6
Views: 2,096
Posted By AlexReynolds
It depends on your experiment. If you're looking...

It depends on your experiment. If you're looking to investigate genes that are proximal to a set of regions, for example (where proximal elements are defined as 1000 bases upstream of the gene) then...
Forum: Bioinformatics 06-03-2013, 02:32 PM
Replies: 6
Views: 2,096
Posted By AlexReynolds
You could use the bedops program, part of the...

You could use the bedops program, part of the BEDOPS suite. It has an asymmetric --range operand that you can use to search for set overlaps with adjusted coordinate ranges:
...
Forum: Bioinformatics 05-21-2013, 11:59 AM
Replies: 1
Views: 1,612
Posted By AlexReynolds
BEDOPS bam2bed...

BEDOPS bam2bed (http://code.google.com/p/bedops/wiki/bam2bed) converts BAM to BED. BEDOPS bedops --everything (http://code.google.com/p/bedops/wiki/bedops) performs a multiset union of BED files.
...
Forum: Bioinformatics 05-21-2013, 11:54 AM
Replies: 3
Views: 7,136
Posted By AlexReynolds
If you want to validate coordinates, the BEDOPS...

If you want to validate coordinates, the BEDOPS bedops application (http://code.google.com/p/bedops/wiki/bedops) can do this, using the --everything...
Showing results 1 to 25 of 45

 


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