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Forum: Bioinformatics 03-08-2012, 10:25 AM
Replies: 4
Views: 10,465
Posted By polyatail
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...
Forum: Bioinformatics 01-25-2012, 11:09 AM
Replies: 6
Views: 11,668
Posted By polyatail
Just at first glance, in your cufflinks run you...

Just at first glance, in your cufflinks run you specify two different parameters that will affect the FPKM calculation.
--upper-quartile-norm --max-mle-iterations 20000
I would try changing...
Forum: Bioinformatics 01-24-2012, 08:27 AM
Replies: 2
Views: 3,250
Posted By polyatail
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...
Forum: Bioinformatics 01-19-2012, 08:47 AM
Replies: 36
Views: 18,907
Posted By polyatail
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...
Forum: Academic/Non-Profit Jobs 01-09-2012, 03:20 PM
Replies: 0
Views: 1,942
Posted By polyatail
Bioinformatics Specialist at New York University School of Medicine

Our laboratory is seeking an energetic and highly motivated Bioinformatics Specialist to work in the area of immunology, virology, and mouse genetics. We are a dynamic and diverse group of...
Forum: Bioinformatics 01-09-2012, 11:13 AM
Replies: 2
Views: 2,674
Posted By polyatail
Are these four samples technical replicates (i.e....

Are these four samples technical replicates (i.e. just different lanes on a flow cell), biological replicates, or different conditions? If they're technical replicates, it is reasonable to combine...
Forum: Bioinformatics 12-27-2011, 02:50 PM
Replies: 21
Views: 40,281
Posted By polyatail
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...
Forum: Bioinformatics 12-27-2011, 02:03 PM
Replies: 21
Views: 40,281
Posted By polyatail
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...
Forum: Bioinformatics 12-27-2011, 11:31 AM
Replies: 13
Views: 6,861
Posted By polyatail
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
-----------
samtools view -F 4 file.bam
print all lines in SAM...
Forum: Bioinformatics 12-17-2011, 02:47 PM
Replies: 2
Views: 4,901
Posted By polyatail
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...
Forum: Bioinformatics 12-12-2011, 07:10 PM
Replies: 9
Views: 2,331
Posted By polyatail
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...
Forum: Bioinformatics 12-09-2011, 02:52 PM
Replies: 8
Views: 6,962
Posted By polyatail
Buccal swab? :)

Buccal swab? :)
Forum: Bioinformatics 12-03-2011, 08:17 AM
Replies: 10
Views: 4,748
Posted By polyatail
I have found the UCSC mirror at...

I have found the UCSC mirror at http://www.ncrna.org useful.
Forum: Bioinformatics 12-02-2011, 10:57 AM
Replies: 4
Views: 4,101
Posted By polyatail
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...
Forum: Bioinformatics 06-03-2011, 08:54 AM
Replies: 7
Views: 3,440
Posted By polyatail
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...
Forum: Bioinformatics 06-01-2011, 02:01 PM
Replies: 7
Views: 4,647
Posted By polyatail
Has anyone found any differences in Cufflinks...

Has anyone found any differences in Cufflinks output when providing a reference via -G at the TopHat step? With or without also providing a reference to Cufflinks?
Forum: Bioinformatics 06-01-2011, 01:56 PM
Replies: 7
Views: 4,647
Posted By polyatail
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...
Forum: Bioinformatics 06-01-2011, 01:45 PM
Replies: 7
Views: 3,440
Posted By polyatail
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...
Forum: Bioinformatics 06-01-2011, 01:35 PM
Replies: 3
Views: 1,865
Posted By polyatail
There are several services. IMG/ER,...

There are several services.

IMG/ER, mentioned above

RAST
http://rast.nmpdr.org/

JCVI
http://www.jcvi.org/cms/research/projects/annotation-service/
Forum: Bioinformatics 05-12-2011, 01:51 PM
Replies: 13
Views: 4,556
Posted By polyatail
* 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...
Forum: Bioinformatics 12-18-2010, 05:15 PM
Replies: 4
Views: 3,086
Posted By polyatail
If you want to use your local installation of...

If you want to use your local installation of boost, I would try:


env LD_LIBRARY_PATH=/path/to/boost /path/to/cufflinks


This should tell the loader to look for the library in your home...
Forum: Bioinformatics 12-17-2010, 02:20 PM
Replies: 4
Views: 3,086
Posted By polyatail
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...
Forum: Bioinformatics 12-17-2010, 02:01 PM
Replies: 2
Views: 1,422
Posted By polyatail
Hi khb, What software did you use to produce...

Hi khb,

What software did you use to produce the alignment? Can you post some of the reads mapping to chrM?


Andrew
Forum: Bioinformatics 12-16-2010, 09:57 PM
Replies: 6
Views: 3,160
Posted By polyatail
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...
Forum: Bioinformatics 12-16-2010, 02:29 PM
Replies: 6
Views: 3,160
Posted By polyatail
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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