Forum: Bioinformatics
06-14-2012, 12:00 AM
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Replies: 4
Views: 3,287
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Forum: Bioinformatics
06-13-2012, 11:54 PM
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Replies: 4
Views: 3,287
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Forum: Bioinformatics
06-13-2012, 01:50 AM
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Replies: 4
Views: 3,287
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Forum: Bioinformatics
06-07-2012, 07:20 AM
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Replies: 7
Views: 2,056
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Forum: Bioinformatics
06-07-2012, 02:20 AM
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Replies: 36
Views: 28,360
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Forum: Bioinformatics
06-07-2012, 12:24 AM
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Replies: 42
Views: 12,681
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Forum: Bioinformatics
06-06-2012, 11:48 PM
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Replies: 7
Views: 2,056
Gene predictors and older short read aligners...
Gene predictors and older short read aligners (pre-SAM). Many tools made within the framework of GMOD use GFF(2/3) to exchange functional information about genomes. You'll find more information on...
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Forum: Bioinformatics
06-06-2012, 04:12 AM
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Replies: 30
Views: 9,619
You wouldn't need to spend that much more money...
You wouldn't need to spend that much more money to get a decent server. We just got a 64 core server (4xAMD 6276) with 512 GB ECC DDR3-1600 RAM (32x16 GB) for ~14 000 €. With 256 GB RAM (32x8 GB), it...
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Forum: Bioinformatics
06-06-2012, 04:01 AM
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Replies: 30
Views: 9,619
Why not buy cloud computing time or run it on...
Why not buy cloud computing time or run it on XSEDE Blacklight or something similar if this is a one-off thing? Or ask someone in your neighbourhood with a beefy server to collaborate on that...
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Forum: Bioinformatics
06-05-2012, 05:27 AM
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Replies: 7
Views: 3,472
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Forum: Bioinformatics
06-05-2012, 01:52 AM
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Replies: 17
Views: 10,707
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Forum: Bioinformatics
06-05-2012, 01:20 AM
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Replies: 17
Views: 10,707
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Forum: Bioinformatics
06-04-2012, 04:53 AM
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Replies: 14
Views: 2,282
Depending on the application, it is often...
Depending on the application, it is often interesting in RNA-Seq to be able to distinguish if a read comes from a sense (i.e. protein coding) or antisense (possibly regulatory) transcript....
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Forum: Bioinformatics
06-04-2012, 03:39 AM
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Replies: 1
Views: 1,866
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Forum: Bioinformatics
06-01-2012, 06:05 AM
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Replies: 2
Views: 2,015
Well, actually they are extending each other....
Well, actually they are extending each other. What you are referring to isn't actually new databases, they are new builds of a database.
A new build consists of the older known entries plus new...
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Forum: Bioinformatics
06-01-2012, 12:51 AM
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Replies: 7
Views: 2,056
I'm not aware of a direct converter, but...
I'm not aware of a direct converter, but theoretically you could feed a BAM into BEDTools BamToBed and push the BED through GenomeTools bed_to_gff3.
I would probably write a converter script myself...
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Forum: Bioinformatics
06-01-2012, 12:33 AM
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Replies: 4
Views: 1,880
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Forum: Bioinformatics
05-29-2012, 07:30 AM
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Replies: 2
Views: 2,860
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Forum: Bioinformatics
05-29-2012, 07:22 AM
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Replies: 4
Views: 2,440
You can checking mapping in a BAM file with...
You can checking mapping in a BAM file with "samtools idxstats file.bam"; that will tell you the number of reads mapping to each chromosome.
If the mapping looks fine, try breaking up all the...
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Forum: Bioinformatics
05-29-2012, 05:33 AM
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Replies: 1
Views: 1,924
I'm not sure what you mean by average, if you...
I'm not sure what you mean by average, if you talk about each position; do you mean each precise position or some kind of window?
Have a look at "bedtools coverage" and "bedtools genomecov"; I...
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Forum: Bioinformatics
05-25-2012, 05:01 AM
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Replies: 3
Views: 3,824
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Forum: Bioinformatics
05-25-2012, 04:37 AM
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Replies: 3
Views: 3,824
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Forum: Bioinformatics
05-25-2012, 04:22 AM
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Replies: 9
Views: 2,956
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Forum: Bioinformatics
05-25-2012, 04:09 AM
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Replies: 1
Views: 2,381
It doesn't make sense to make a GTF file for a...
It doesn't make sense to make a GTF file for a transcript fasta file, like yours. You use a GTF file to describe the transcript annotations for a genome fasta file.
I'm not working on human, so...
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Forum: Bioinformatics
05-25-2012, 03:58 AM
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Replies: 9
Views: 2,956
:confused: If you are simulating reads, why...
:confused: If you are simulating reads, why without errors? If you are developing an algorithm or heuristic that should deal with real reads, I don't see the point... because they will behave quite...
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