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Forum: RNA Sequencing 03-07-2013, 09:37 AM
Replies: 0
Views: 2,456
Posted By jebe
How do you get the gene length that htseq-count is using?

Hi, I have human rna-seq data and I'm using htseq-count to get the number of reads that map to Ensembl genes. I believe htseq-count uses a union model to summarize the transcripts into genes. How...
Forum: Bioinformatics 07-01-2010, 11:42 AM
Replies: 0
Views: 1,659
Posted By jebe
Strange cuffdiff result (disagreement between tracking and diff files)

I ran cuffdiff specifying the ensembl gtf across 4 mRNA-seq samples. The output from 0_1_gene_exp.diff for gene GNAS is as follows:

ENSG00000087460 GNAS chr20:56848167-56919644 NOTEST 0 ...
Forum: Bioinformatics 07-01-2010, 11:30 AM
Replies: 34
Views: 35,591
Posted By jebe
Converting FPKM from Cufflinks to raw counts for DESeq

How to I convert the FPKM values output by Cufflinks in genes.expr to raw counts to import into DESeq?
Forum: Bioinformatics 03-18-2010, 12:42 PM
Replies: 47
Views: 30,224
Posted By jebe
cuffcompare tracking file

The output from cuffcompare stdout.tracking, according to the manual and replies on this website is as follows:

qJ:<gene_id>|<transcript_id>|<FMI>|<FPKM>|<conf_lo >|<conf_hi>|<read coverage>

In...
Forum: Bioinformatics 03-03-2010, 11:32 AM
Replies: 47
Views: 30,224
Posted By jebe
cuffdiff considers only X, Y, and MT loci

Hi,

I ran tophat using the h_sapiens_37_asm index and converted the accepted_hits.sam file's chromosomes accessions to their corresponding number/letter (1,2,X,Y,MT). I wanted the chromosome...
Forum: RNA Sequencing 01-26-2010, 12:29 PM
Replies: 0
Views: 3,034
Posted By jebe
How to convert cufflinks output to raw counts

I would like to calculate raw counts for each cufflinks transcript. I can convert to reads per million by multiplying by the length of the transcript, but I'm not sure how what the cufflinks...
Forum: Bioinformatics 01-07-2010, 09:00 AM
Replies: 42
Views: 16,595
Posted By jebe
cuffcompare class codes

What does the class code p stand for? A reference to it is also not in the manual.
Forum: Academic/Non-Profit Jobs 11-06-2009, 01:09 PM
Replies: 0
Views: 2,006
Posted By jebe
Post-doctoral research fellow in Translational Bioinformatics, Boston University

We are seeking a creative and motivated postdoctoral fellow to join our lab within the Department of Medicine and participate in our active research program aimed at using genomic approaches to...
Forum: Academic/Non-Profit Jobs 11-05-2009, 06:54 AM
Replies: 0
Views: 2,209
Posted By jebe
Research Technician, Next-Generation Sequencing, Boston University School of Medicine

Description:
A full-time position is available for an experienced research technician with a background in genomics and/or molecular biology. Experience with next-generation DNA sequencing...
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