Forum: RNA Sequencing
03-14-2014, 12:53 PM
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Replies: 0
Views: 2,416
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Forum: RNA Sequencing
02-07-2014, 11:46 AM
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Replies: 0
Views: 1,512
Wrong exon number information from tophat-fusion
I posted this question in "BioInformatics" as well to someone who experienced similar problem with no answers. Any solutions from the RNASequencing forum?
It appears to me that somehow tophat...
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Forum: Bioinformatics
02-07-2014, 11:42 AM
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Replies: 1
Views: 1,543
messed up exon information from tophat-fusion
I also experienced similar problem with well known fusion.
Expected fusion in my sample is TMPRSS2(Exon1) with ERG. What I obtain is TMPRSS2 (exon14) with ERG which doesn't make sense.
Is there...
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Forum: Bioinformatics
11-11-2013, 06:10 PM
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Replies: 2
Views: 3,306
difference between rr ff and rf reads
Hi:
I am wondering which fusion should I prioritize from a couple of candidates.
As you know tophat fusion generates a list with the direction of fusion mentioned as well. I am not a biologist...
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Forum: RNA Sequencing
08-26-2013, 11:32 AM
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Replies: 1
Views: 1,617
how to look for known fusion in fastq file
Hello:
I have an internal data for NCI-h660 file with 8m mapped pairs (HiSeq, 50bp paired end data) and I have an external dataset (4m mapped pairs, 50 bp paired end generated on GAII).
...
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Forum: RNA Sequencing
08-15-2013, 12:24 PM
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Replies: 9
Views: 4,464
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Forum: RNA Sequencing
08-15-2013, 12:02 PM
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Replies: 9
Views: 4,464
So I ran the following perl script:
...
So I ran the following perl script:
https://bitbucket.org/jesseerdmann/fairview-galaxy-dist/raw/8e6e7a346284c7c261c951998b0138e82f540f43/tools/msi/pe-sync-2-files.pl
and it says: "passed full...
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Forum: RNA Sequencing
08-15-2013, 09:14 AM
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Replies: 9
Views: 4,464
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Forum: RNA Sequencing
08-15-2013, 08:49 AM
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Replies: 9
Views: 4,464
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Forum: RNA Sequencing
07-28-2013, 04:52 PM
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Replies: 1
Views: 1,414
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Forum: RNA Sequencing
07-03-2013, 10:11 AM
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Replies: 0
Views: 1,346
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Forum: RNA Sequencing
06-11-2013, 11:34 AM
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Replies: 1
Views: 2,572
genes.fpkm_tracking (Coverage column)
In the genes.fpkm_tracking file, why is the "coverage" for the gene not reported from cufflinks?
I understand to get the fpkm_per_gene, transcript level fpkm is summed up. How about coverage...
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Forum: RNA Sequencing
06-09-2013, 06:02 PM
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Replies: 2
Views: 1,936
memory error: tophat-fusion-post
I have ~400 samples where I ran tophat2 fusion. Now I am trying to run tophat-fusion-post which gives the following error:
Traceback (most recent call last):
File...
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Forum: RNA Sequencing
05-05-2013, 08:10 PM
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Replies: 3
Views: 4,525
Error with RNA-SeQC
Hi,
I used following 4 steps to get sequencing statistics from RNASeqC but I get error, could anyone help me understand and get rid of this error?
Thanks.
RNA-SeQC v1.1.7 05/14/12
Creating...
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Forum: RNA Sequencing
04-29-2013, 12:44 PM
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Replies: 0
Views: 1,383
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Forum: Bioinformatics
04-23-2013, 08:09 AM
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Replies: 34
Views: 13,991
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Forum: Bioinformatics
04-22-2013, 09:51 AM
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Replies: 34
Views: 13,991
how to modify 1.fq to write bamfilename_1.fq?
Hi Richard,
How can I modify "1.fq" and "2.fq" to write instead bamfilename_1.fq and bamfilename_2.fq as I have many bam files and I want to preserve the name of the file where fastq files are...
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Forum: RNA Sequencing
04-16-2013, 01:13 PM
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Replies: 0
Views: 1,604
Estimate tophat2 parameters from rnaseq data?
I have some pre-computed bam files which I need to run tophat2 fusion search. Can anyone guide me as to how to use these RNA metrics to determine tophat2 parameters e.g. mate_inner_dist,...
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Forum: RNA Sequencing
04-15-2013, 01:02 PM
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Replies: 5
Views: 2,108
Hi Daniel,
I am referring to the 27 fusions...
Hi Daniel,
I am referring to the 27 fusions that are mentioned to be known and/or validated by RT-PCR as mentioned in the paper.
I didn't use the same version of software as in the paper. I...
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Forum: RNA Sequencing
04-15-2013, 09:03 AM
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Replies: 5
Views: 2,108
Missing 4 fusions using tophat2
Hi Daniel,
It seems you mis understood my question. the question was how to modify tophat2 or tophat-fusion-post parameters to find the 4 missing fusions which were found using previous versions...
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Forum: RNA Sequencing
04-14-2013, 08:59 PM
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Replies: 5
Views: 2,108
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Forum: RNA Sequencing
04-02-2013, 07:32 AM
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Replies: 5
Views: 2,772
tophat-fusion-post: KeyError: 'score'
Hello, I am tophat-fusion-post. My job ran fine until the very end where I get the error ("Score") as below.
I get 6898 fusions in potential_fusion.txt with the command:
> tophat-fusion-post -p...
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Forum: Bioinformatics
03-05-2012, 07:43 AM
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Replies: 0
Views: 2,262
"Bcftools mpileup" removes marked duplicates?
Hey,
My question is does samtools mpileup automatically removed duplicates from test.marked.bam output from Picard/MarkDuplicates?
I used Picard Tools to create: test.marked.bam
Then I use ...
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Forum: Bioinformatics
02-28-2012, 05:59 PM
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Replies: 2
Views: 2,266
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Forum: Bioinformatics
02-19-2012, 06:04 PM
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Replies: 0
Views: 1,329
Marking duplicates and comparing 2 WE samples?
Hey,
Two follow-up questions for my WholeExome Analysis: :p
1) I used Picard "MarkDuplicates" to mark duplicates and called bam as "marked.bam". I used snpeff to annotate snps and indels etc....
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