Forum: Bioinformatics
03-08-2012, 10:25 AM
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Replies: 4
Views: 10,629
You might get something out of this paper, and...
You might get something out of this paper, and its supplemental:
http://www.ncbi.nlm.nih.gov/pubmed/20444704
They did a lot of trial and error to find the best way to do bacterial RNA-Seq on in...
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Forum: Bioinformatics
01-25-2012, 11:09 AM
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Replies: 6
Views: 11,725
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Forum: Bioinformatics
01-24-2012, 08:27 AM
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Replies: 2
Views: 3,282
I've never tried these tools on bacterial...
I've never tried these tools on bacterial RNA-seq, but it's my understanding that they were designed with eukaryotes in mind. TopHat, for example, aligns reads across splice junctions which...
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Forum: Bioinformatics
01-19-2012, 08:47 AM
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Replies: 36
Views: 18,998
You can get this pretty easily from the UCSC...
You can get this pretty easily from the UCSC table browser (http://genome.ucsc.edu/cgi-bin/hgTables).
Select "All Tables" from the group drop-down list
Select the "rmsk" table from the table...
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Forum: Academic/Non-Profit Jobs
01-09-2012, 03:20 PM
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Replies: 0
Views: 1,972
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Forum: Bioinformatics
01-09-2012, 11:13 AM
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Replies: 2
Views: 2,705
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Forum: Bioinformatics
12-27-2011, 02:50 PM
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Replies: 21
Views: 40,513
Check out this paper's supplemental:
Cabili...
Check out this paper's supplemental:
Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global...
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Forum: Bioinformatics
12-27-2011, 02:03 PM
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Replies: 21
Views: 40,513
I'm curious about this too. Cuffmerge...
I'm curious about this too. Cuffmerge (apparently) merges GTFs by converting them to SAM and running Cufflinks on the resulting fake alignments to produce new transcripts. In what ways is this...
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Forum: Bioinformatics
12-27-2011, 11:31 AM
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Replies: 13
Views: 6,980
Something like this might work.
samtools...
Something like this might work.
samtools view -F 4 file.bam | awk '{printf $1"\n"}' | sort | uniq -d | wc -l
Explanation
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samtools view -F 4 file.bam
print all lines in SAM...
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Forum: Bioinformatics
12-17-2011, 02:47 PM
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Replies: 2
Views: 4,929
The fragment length is the size of the piece of...
The fragment length is the size of the piece of DNA that was sequenced, which is generally significantly longer than the length of the reads. In a paired end run, you can estimate the fragment length...
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Forum: Bioinformatics
12-12-2011, 07:10 PM
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Replies: 9
Views: 2,359
There are a number of tools out there that...
There are a number of tools out there that attempt to cluster or classify reads or contigs by sequence-intrinsic properties (i.e. k-mers, protein domains). Check out TETRA, WebCarma, TACOA or...
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Forum: Bioinformatics
12-09-2011, 02:52 PM
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Replies: 8
Views: 7,056
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Forum: Bioinformatics
12-03-2011, 08:17 AM
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Replies: 10
Views: 4,787
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Forum: Bioinformatics
12-02-2011, 10:57 AM
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Replies: 4
Views: 4,125
From what I can tell, -g is passed by TopHat...
From what I can tell, -g is passed by TopHat directly to bowtie as the -k (maximum number of alignments reported) and -m (suppress all alignments if >n are found) parameters. As each mate is aligned...
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Forum: Bioinformatics
06-03-2011, 08:54 AM
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Replies: 7
Views: 3,482
Couldn't agree more. Especially if your storage...
Couldn't agree more. Especially if your storage is lacking, and those 48 cores are pushing out a lot of data (i.e. sequence alignment, BAM files), IO will be a problem. With 192 GB, you'd even have...
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Forum: Bioinformatics
06-01-2011, 02:01 PM
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Replies: 7
Views: 4,703
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Forum: Bioinformatics
06-01-2011, 01:56 PM
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Replies: 7
Views: 4,703
From the manual, it sounds like it will output...
From the manual, it sounds like it will output all provided reference transcripts in addition to any novel isoforms. If I'm understanding your question correctly, it sounds like you'd be able to...
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Forum: Bioinformatics
06-01-2011, 01:45 PM
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Replies: 7
Views: 3,482
If most of what you're doing is aligning reads...
If most of what you're doing is aligning reads back to a reference genome, a highly-threaded sequence aligner will be quickest with a bunch of cores. If you're doing genome assembly, most of the...
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Forum: Bioinformatics
06-01-2011, 01:35 PM
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Replies: 3
Views: 1,892
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Forum: Bioinformatics
05-12-2011, 01:51 PM
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Replies: 13
Views: 4,600
* If you're using paired-end reads, check the...
* If you're using paired-end reads, check the cufflinks log to be sure they're aligned and recognized as PE. In other threads, that wasn't the case.
* Tune the anchor length and multiplicity (-a...
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Forum: Bioinformatics
12-18-2010, 05:15 PM
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Replies: 4
Views: 3,111
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Forum: Bioinformatics
12-17-2010, 02:20 PM
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Replies: 4
Views: 3,111
Hi,
What Linux are you running? I would...
Hi,
What Linux are you running? I would start by checking the libraries cufflinks is compiled to require by running:
ldd /path/to/cufflinks
And the location of the installed boost libraries...
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Forum: Bioinformatics
12-17-2010, 02:01 PM
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Replies: 2
Views: 1,446
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Forum: Bioinformatics
12-16-2010, 09:57 PM
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Replies: 6
Views: 3,188
From http://samtools.sourceforge.net/SAM1.pdf,...
From http://samtools.sourceforge.net/SAM1.pdf, the name of both mates in a pair must be the same. So while the two reads you mentioned are certainly paired, they aren't matched up in Cufflinks...
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Forum: Bioinformatics
12-16-2010, 02:29 PM
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Replies: 6
Views: 3,188
Hi Lindy,
Can you post a few lines of the...
Hi Lindy,
Can you post a few lines of the input SAM file you're feeding Cufflinks? You can retrieve it from a BAM file with:
samtools view accepted_hits.bam | tail -n +25 | head -n 10
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