search

Genomicus / bedtools

Automatically exported from code.google.com/p/bedtools
0 stars 0 forks source link

annotateBed and names options #126

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Using the annotateBed with the option -both and -names, I have a small bug of 
field separator for the names (BEDTools v2.16.2).

The separator between the _ctn and _pct is missing .. and can create problems 
in further analysis (parser, ...)

#                       precursor_miRNA_cnt precursor_miRNA_pctrmsk_rRNA_cnt    rmsk_rRNA_pctrfam_cn
t   rfam_pctrmsk_cnt    rmsk_pctcoding_gene_cnt coding_gene_pct
chr1    44302332    44302351    1955_1  2626    -   0   0.000000    0   0.000000    0   0.000000    1   1.000000
    0   0.000000    
c

Regards
Nicolas

Original issue reported on code.google.com by nicolas....@gmail.com on 11 Jun 2012 at 8:26

GoogleCodeExporter commented 9 years ago 
Thanks for reporting this, I'll have a look today.

Original comment by aaronqui...@gmail.com on 12 Jun 2012 at 10:58

GoogleCodeExporter commented 9 years ago 
You're welcome !
Btw, i had a question about memory usage of annotateBed
I run annotateBed with a bam file of 10 millions of reads and 5 annotations  
files.
It took more than 250Go of RAM !
Can you just briefly tell me which part is loaded in memory, and if i can  
reproduce annotateBed using, for instance, several intersectBed processes ?
thank you very much

nicolas

Le , bedtools@googlecode.com a �crit :

Original comment by nicolas....@gmail.com on 13 Jun 2012 at 9:57

GoogleCodeExporter commented 9 years ago 
This has been fixed in the github repository and will be part of the next 
release.

Original comment by aaronqui...@gmail.com on 19 Jun 2012 at 4:57